From 0e8c17c0f4dfafd69f457ac753b3d418e55acec2 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 2 Oct 2023 13:31:45 +0100 Subject: [PATCH 01/17] Dropped superfluous dependency on st::api::request --- t/util.pm | 6 ------ 1 file changed, 6 deletions(-) diff --git a/t/util.pm b/t/util.pm index 7b3ea3764..0f688bf55 100644 --- a/t/util.pm +++ b/t/util.pm @@ -4,7 +4,6 @@ use Moose; use File::Temp qw{ tempdir }; use Readonly; use File::Path qw(make_path); -use npg::api::request; Readonly::Scalar my $NFS_STAGING_DISK => q{/nfs/sf45}; @@ -116,9 +115,4 @@ ENDXML close $fh; } -# ensure that the environment variables do not get passed around -sub DEMOLISH { - $ENV{ npg::api::request->cache_dir_var_name() } = q{}; -} - 1; From 425409df770f2921fd0a1bfe726bf676220c62e6 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 4 Oct 2023 18:41:05 +0100 Subject: [PATCH 02/17] MANIFEST - drop listing of non-existing files --- MANIFEST | 2 -- 1 file changed, 2 deletions(-) diff --git a/MANIFEST b/MANIFEST index 1c16bcc2a..f9d13a5d3 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1,4 +1,3 @@ -.github/workflows/testing_and_building_repo.yml bin/npg_pipeline_analysis_runner bin/npg_pipeline_archival_runner bin/npg_pipeline_central @@ -78,7 +77,6 @@ lib/npg_pipeline/validation/s3.pm MANIFEST This list of files README README.md -scripts/install_npg_perl_dependencies.sh scripts/jgf2gml t/00-critic.t t/00-distribution.t From 5b2bd6858ecce421775cf92726120296da39b696 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 13 Oct 2023 16:14:48 +0100 Subject: [PATCH 03/17] Removed listing of previously deleted files from MANIFEST --- MANIFEST | 2 -- 1 file changed, 2 deletions(-) diff --git a/MANIFEST b/MANIFEST index 1c16bcc2a..f9d13a5d3 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1,4 +1,3 @@ -.github/workflows/testing_and_building_repo.yml bin/npg_pipeline_analysis_runner bin/npg_pipeline_archival_runner bin/npg_pipeline_central @@ -78,7 +77,6 @@ lib/npg_pipeline/validation/s3.pm MANIFEST This list of files README README.md -scripts/install_npg_perl_dependencies.sh scripts/jgf2gml t/00-critic.t t/00-distribution.t From bd13f02ac60812bf0dc05e099c47283a1ae6df72 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 18 Oct 2023 13:27:37 +0100 Subject: [PATCH 04/17] Removed provisions for inline indexes. Removed provisions for inline indexes in creating p4stage1 jobs. These indexes have not been used for the last 6 years. --- .../function/p4_stage1_analysis.pm | 72 +++---------------- 1 file changed, 8 insertions(+), 64 deletions(-) diff --git a/lib/npg_pipeline/function/p4_stage1_analysis.pm b/lib/npg_pipeline/function/p4_stage1_analysis.pm index c747f455d..686b71c68 100644 --- a/lib/npg_pipeline/function/p4_stage1_analysis.pm +++ b/lib/npg_pipeline/function/p4_stage1_analysis.pm @@ -197,22 +197,13 @@ sub _get_index_lengths { my ( $self, $lane_lims ) = @_; my @index_length_array; - - if ($lane_lims->inline_index_exists) { - # Tradis run - treat as a special case - my $index_start = $lane_lims->inline_index_start; - my $index_end = $lane_lims->inline_index_end; - if ($index_start && $index_end) { - push @index_length_array, $index_end - $index_start + 1; - } - } else { - my $n = 0; - my @cycle_counts = $self->read_cycle_counts(); - my @reads_indexed = $self->reads_indexed(); - foreach my $n (0..$#cycle_counts) { - if ($reads_indexed[$n]) { push @index_length_array, $cycle_counts[$n]; } - } + my $n = 0; + my @cycle_counts = $self->read_cycle_counts(); + my @reads_indexed = $self->reads_indexed(); + foreach my $n (0..$#cycle_counts) { + if ($reads_indexed[$n]) { push @index_length_array, $cycle_counts[$n]; } } + return \@index_length_array; } @@ -221,7 +212,7 @@ sub _get_index_lengths { # Determine parameters for the lane from LIMS information and create the hash from which the p4 stage1 # analysis param_vals file will be generated. Generate the vtfp/viv commands using this param_vals file. ######################################################################################################### -sub _generate_command_params { ## no critic (Subroutines::ProhibitExcessComplexity) +sub _generate_command_params { my ($self, $lane_lims, $tag_list_file, $lane_product) = @_; my %p4_params = ( samtools_executable => q{samtools}, @@ -302,52 +293,6 @@ sub _generate_command_params { ## no critic (Subroutines::ProhibitExcessComplexi $p4_params{i2b_bc_qual_val} = q[tq]; } - if($lane_lims->inline_index_exists) { - my $index_start = $lane_lims->inline_index_start; - my $index_end = $lane_lims->inline_index_end; - my $index_read = $lane_lims->inline_index_read; - - if ($index_start && $index_end && $index_read) { - $self->info(q{P4 stage1 analysis of a lane with inline indexes}); - - my($first, $final) = $self->read1_cycle_range(); - if ($index_read == 1) { - $p4_params{i2b_bc_read} = 1; - $index_start += ($first-1); - $index_end += ($first-1); - $p4_params{i2b_first_index_0} = $index_start; - $p4_params{i2b_final_index_0} = $index_end; - $p4_params{i2b_first_index_1} = $first; - $p4_params{i2b_final_index_1} = $index_start-1; - $p4_params{i2b_first_0} = $index_end+1; - $p4_params{i2b_final_0} = $final; - if ($self->is_paired_read()) { - ($first, $final) = $self->read2_cycle_range(); - $p4_params{i2b_first_1} = $first; - $p4_params{i2b_final_1} = $final; - } - } elsif ($index_read == 2) { - $p4_params{i2b_bc_read} = 2; - $self->is_paired_read() or $self->logcroak(q{Inline index read (2) does not exist}); - $p4_params{i2b_first_0} = $first; - $p4_params{i2b_final_0} = $final; - ($first, $final) = $self->read2_cycle_range(); - $index_start += ($first-1); - $index_end += ($first-1); - $p4_params{i2b_first_index_0} = $index_start; - $p4_params{i2b_final_index_0} = $index_end; - $p4_params{i2b_first_index_1} = $first; - $p4_params{i2b_final_index_1} = $index_start-1; - $p4_params{i2b_first_1} = $index_end+1; - $p4_params{i2b_final_1} = $final; - } else { - $self->logcroak("Invalid inline index read ($index_read)"); - } - $p4_params{i2b_sec_bc_seq_val} = q{br}; - $p4_params{i2b_sec_bc_qual_val} = q{qr}; - } - } - if($self->_is_duplexseq($lane_lims)) { $self->info(q{P4 stage1 analysis of a Duplex-Seq lane}); @@ -417,8 +362,7 @@ sub _generate_command_params { ## no critic (Subroutines::ProhibitExcessComplexi } ### TODO: remove this read length comparison if biobambam will handle this case. Check clip reinsertion. - if($self->is_paired_read() && !$lane_lims->inline_index_exists) { - # omit BamAdapterFinder for inline index + if($self->is_paired_read()) { my @range1 = $self->read1_cycle_range(); my $read1_length = $range1[1] - $range1[0] + 1; my @range2 = $self->read2_cycle_range(); From 8dcbb61242aef132163d66a933628e69513e43dc Mon Sep 17 00:00:00 2001 From: Carol Scott Date: Thu, 19 Oct 2023 17:59:17 +0100 Subject: [PATCH 05/17] Add in use of autosome target regions for BGE libraries in seq_alignment --- Changes | 2 ++ lib/npg_pipeline/function/seq_alignment.pm | 17 ++++++++++++----- 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/Changes b/Changes index 12485fd4a..375d4eb77 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,8 @@ LIST OF CHANGES --------------- + - Add in use of autosome target regions for BGE libraries in seq_alignment + release 67.0.0 - Turn off spatial filter QC check for NovaSeqX - Switch to Perlbrew to obtain multiple Perl versions diff --git a/lib/npg_pipeline/function/seq_alignment.pm b/lib/npg_pipeline/function/seq_alignment.pm index 040da7a1b..b546b68bf 100644 --- a/lib/npg_pipeline/function/seq_alignment.pm +++ b/lib/npg_pipeline/function/seq_alignment.pm @@ -36,6 +36,7 @@ Readonly::Scalar my $PFC_MARKDUP_OPT_DIST => q{2500}; # distance in pix Readonly::Scalar my $NON_PFC_MARKDUP_OPT_DIST => q{100}; # distance in pixels for optical duplicate detection on non-patterned flowcells Readonly::Scalar my $BWA_MEM_MISMATCH_PENALTY => q{5}; Readonly::Scalar my $SKIP_MARKDUP_METRICS => 1; +Readonly::Scalar my $AUTO_COV_THRESHOLD => 1; around 'markdup_method' => sub { my $orig = shift; @@ -371,16 +372,22 @@ sub _alignment_command { ## no critic (Subroutines::ProhibitExcessComplexity) # handle extra stats file for aligned data with reference regions file my $do_target_regions_stats = 0; - if ($do_target_alignment && !$spike_tag && !$human_split && !$do_gbs_plex && !$do_rna) { + if ($do_target_alignment && !$spike_tag && !$do_gbs_plex && !$do_rna) { + my $target_path = $self->_ref($dp, $TARGET_REGIONS_DIR); + my $target_autosome_path = $self->_ref($dp, $TARGET_AUTOSOME_REGIONS_DIR); + if($self->_do_bait_stats_analysis($dp)){ $p4_param_vals->{target_regions_file} = $self->_bait($rpt_list)->target_intervals_path(); - push @{$p4_ops->{prune}}, 'foptgt.*samtools_stats_F0.*_target_autosome.*-'; $do_target_regions_stats = 1; + if ( $l->library_type && ($l->library_type =~ /BGE/smx) && $target_autosome_path ) { + $p4_param_vals->{target_autosome_regions_file} = $target_autosome_path.q(.interval_list); + $p4_param_vals->{stats_filter__cov_threshold_autosome} = $AUTO_COV_THRESHOLD; + } else { + push @{$p4_ops->{prune}}, 'foptgt.*samtools_stats_F0.*_target_autosome.*-'; + } } else { - my $target_path = $self->_ref($dp, $TARGET_REGIONS_DIR); - my $target_autosome_path = $self->_ref($dp, $TARGET_AUTOSOME_REGIONS_DIR); - if ($target_path) { + if ($target_path && !$human_split) { $p4_param_vals->{target_regions_file} = $target_path.q(.interval_list); $do_target_regions_stats = 1; if ($target_autosome_path) { From dee7fd7ca31d96fa37f0c4093598dce1dc53e198 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 26 Oct 2023 12:17:38 +0100 Subject: [PATCH 06/17] Update Build.PL, drop dependency on st::api::request --- Build.PL | 1 - 1 file changed, 1 deletion(-) diff --git a/Build.PL b/Build.PL index a522cc74e..ca72e34b8 100755 --- a/Build.PL +++ b/Build.PL @@ -98,7 +98,6 @@ my $builder = $class->new( 'npg_qc::illumina::interop::parser' => 0, 'st::api::lims' => 0, 'st::api::lims::ml_warehouse' => 0, - 'npg::api::request' => 0, 'npg::samplesheet' => 0, 'WTSI::DNAP::Utilities::Loggable' => 0, 'WTSI::DNAP::Warehouse::Schema' => 0, From 4e32d212fa0342f64a67106714762767e4aa8de4 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 26 Oct 2023 12:01:19 +0100 Subject: [PATCH 07/17] Stop tests creating data in the source tree. t/20-function-pp_data_to_irods_archiver.t - set up a test runfolder in a temporary directory. t/15-product-release-irods.t - correctly use test utility library function. --- t/15-product-release-irods.t | 2 +- t/20-function-pp_data_to_irods_archiver.t | 13 +++++++++---- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/t/15-product-release-irods.t b/t/15-product-release-irods.t index fe73d5c11..b716a721d 100644 --- a/t/15-product-release-irods.t +++ b/t/15-product-release-irods.t @@ -82,7 +82,7 @@ subtest 'destination collection - instance methods and attributes' => sub { q[/seq/26219], 'flat run-level archive'); my $util = t::util->new(); - my $paths = $util->create_runfolder( + my $paths = $util->create_runfolder(undef, {runfolder_name => '220128_HX9_43416_A_HHCCCCCX2'}); my $path = $paths->{runfolder_path}; copy 't/data/hiseqx/43416_runParameters.xml', $path .q[/runParameters.xml]; diff --git a/t/20-function-pp_data_to_irods_archiver.t b/t/20-function-pp_data_to_irods_archiver.t index 94295fdbd..f5c8de77f 100644 --- a/t/20-function-pp_data_to_irods_archiver.t +++ b/t/20-function-pp_data_to_irods_archiver.t @@ -6,10 +6,15 @@ use JSON; use File::Slurp; use Test::More tests => 4; use Test::Exception; -use File::Copy; +use File::Copy::Recursive qw(fcopy dircopy); +use File::Temp qw(tempdir); -my $runfolder_path = 't/data/novaseq/200709_A00948_0157_AHM2J2DRXX'; -my $bbc_path = join q[/], getcwd(), $runfolder_path, +my $tdir = tempdir(CLEANUP => 1); +my $rf_name = '200709_A00948_0157_AHM2J2DRXX'; +my $runfolder_path = join q[/], $tdir, $rf_name; +dircopy("t/data/novaseq/$rf_name", $runfolder_path); + +my $bbc_path = join q[/], $runfolder_path, 'Data/Intensities/BAM_basecalls_20200710-105415'; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = join q[/], $bbc_path, @@ -33,7 +38,7 @@ my %init = ( } ); -copy 'data/config_files/log4perl_publish_tree.conf', $init{'conf_path'}; +fcopy 'data/config_files/log4perl_publish_tree.conf', $init{'conf_path'}; my $syslog_config = join q[/], $init{'conf_path'}, 'log4perl_publish_tree.conf'; subtest 'local flag' => sub { From 4385638d1c022d55f68c03b258254bf5375b0919 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 26 Oct 2023 18:10:26 +0100 Subject: [PATCH 08/17] Simplified and clarified products' generation. Removed a check for rapid runs when deciding wheather to merge, this is made possible by https://github.com/wtsi-npg/npg_tracking/pull/770 Clarified and added documentation and comments. Refactored the code so that the builder method for the 'products' attribute is shorter and easier to understand - prep for partial merge implementation. --- lib/npg_pipeline/base.pm | 105 +++++++++++++++++++++++---------------- 1 file changed, 62 insertions(+), 43 deletions(-) diff --git a/lib/npg_pipeline/base.pm b/lib/npg_pipeline/base.pm index 7b4b76d97..6ab0ce468 100644 --- a/lib/npg_pipeline/base.pm +++ b/lib/npg_pipeline/base.pm @@ -174,8 +174,9 @@ sub random_string { =head2 positions -A sorted array of lanes (positions) this pipeline will be run on. -Defaults to positions specified in LIMs. +A sorted list of lanes (positions) this pipeline will analyse. +This list is set from the values supplied by the C attribute. If +lanes are not set explicitly, defaults to positions specified in LIMS. =cut @@ -206,8 +207,8 @@ sub _build_general_values_conf { =head2 merge_lanes -Tells p4 stage2 (seq_alignment) to merge lanes (at their plex level if plexed) -and to run its downstream tasks as corresponding compositions. +Tells p4 stage2 (seq_alignment) to merge all lanes (at their plex level +if plexed) and to run its downstream tasks using corresponding compositions. =cut @@ -217,13 +218,13 @@ has q{merge_lanes} => ( lazy => 1, predicate => q{has_merge_lanes}, builder => q{_build_merge_lanes}, - documentation => q{Tells p4 stage2 (seq_alignment) to merge lanes } . + documentation => q{Tells p4 stage2 (seq_alignment) to merge all lanes } . q{(at their plex level if plexed) and to run its } . - q{downstream tasks as corresponding compositions}, + q{downstream tasks using corresponding compositions}, ); sub _build_merge_lanes { my $self = shift; - return $self->all_lanes_mergeable && !$self->is_rapid_run(); + return $self->all_lanes_mergeable; } =head2 lims @@ -316,6 +317,13 @@ sub get_tag_index_list { =head2 products +Two arrays of npg_pipeline::product objects, one for lanes, hashed under +the 'lanes' key, another for end products, including, where relevant, tag +zero products, hashed under the 'data_products' key. + +If product_rpt_list attribute is set, the 'lanes' key maps to an empty +array. + =cut has q{products} => ( @@ -327,48 +335,59 @@ has q{products} => ( sub _build_products { my $self = shift; - my $selected_lanes = $self->has_product_rpt_list ? 0 : - ((join q[], $self->positions) ne - (join q[], map {$_->position} $self->lims->children())); - - my $lims2product = sub { - my $lims = shift; - return npg_pipeline::product->new( - rpt_list => npg_tracking::glossary::rpt->deflate_rpt($lims), - lims => $lims, - selected_lanes => $selected_lanes); - }; - my @lane_lims = (); - if (!$self->has_product_rpt_list) { - @lane_lims = map { $self->lims4lane($_) } $self->positions; - } + my @data_lims = (); - my @data_products; - if ($self->has_product_rpt_list || $self->merge_lanes) { - @data_products = - map { - npg_pipeline::product->new(lims => $_, - rpt_list => $_->rpt_list, - selected_lanes => $selected_lanes) - } - $self->has_product_rpt_list ? ($self->lims) : - $self->lims->aggregate_xlanes($self->positions); + if ($self->has_product_rpt_list) { + @data_lims = ($self->lims); } else { - my @lims = (); - foreach my $lane (@lane_lims) { - if ($self->is_indexed && $lane->is_pool) { - push @lims, $lane->children; - push @lims, $lane->create_tag_zero_object(); - } else { - push @lims, $lane; + my @positions = $self->positions; + @lane_lims = map { $self->lims4lane($_) } @positions; + if ($self->merge_lanes) { + @data_lims = $self->lims->aggregate_xlanes(@positions); + } else { + foreach my $lane (@lane_lims) { + if ($self->is_indexed && $lane->is_pool) { + push @data_lims, $lane->children, $lane->create_tag_zero_object(); + } else { + push @data_lims, $lane; + } } } - @data_products = map { $lims2product->($_) } @lims; } - return { 'data_products' => \@data_products, - 'lanes' => [map { $lims2product->($_) } @lane_lims] }; + return { + 'data_products' => [map { $self->_lims_object2product($_) } @data_lims], + 'lanes' => [map { $self->_lims_object2product($_) } @lane_lims] + }; +} + +##### +# The boolean flag below defines whether lane numbers are explicitly +# listed in directory and file names for merged products. It is set +# to true whenever a subset of all available lanes is analysed. +has q{_selected_lanes} => ( + isa => q{Bool}, + is => q{ro}, + lazy_build => 1, +); +sub _build__selected_lanes { + my $self = shift; + if (!$self->has_product_rpt_list) { + return ((join q[], $self->positions) ne + (join q[], map {$_->position} $self->lims->children())) + } + return; +} + +sub _lims_object2product { + my ($self, $lims) = @_; + return npg_pipeline::product->new( + rpt_list => $lims->rpt_list ? $lims->rpt_list : + npg_tracking::glossary::rpt->deflate_rpt($lims), + lims => $lims, + selected_lanes => $self->_selected_lanes + ) } __PACKAGE__->meta->make_immutable; @@ -424,7 +443,7 @@ Marina Gourtovaia =head1 LICENSE AND COPYRIGHT -Copyright (C) 2014,2015,2016,2017,2018,2019,2020 Genome Research Ltd. +Copyright (C) 2014,2015,2016,2017,2018,2019,2020,2023 Genome Research Ltd. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by From 2a9e2bc7d50438b18e6a84bfddb9cbf719503914 Mon Sep 17 00:00:00 2001 From: mgcam Date: Mon, 30 Oct 2023 22:07:54 +0000 Subject: [PATCH 09/17] Added a test to expose a problem with ref cache (#803) --- MANIFEST | 4 + t/20-function-seq_alignment.t | 109 +- t/data/novaseqx_47539/README.md | 7 + t/data/novaseqx_47539/RunInfo.xml | 3162 +++++++++++++++++++ t/data/novaseqx_47539/RunParameters.xml | 79 + t/data/novaseqx_47539/samplesheet_47539.csv | 82 + 6 files changed, 3442 insertions(+), 1 deletion(-) create mode 100644 t/data/novaseqx_47539/README.md create mode 100644 t/data/novaseqx_47539/RunInfo.xml create mode 100644 t/data/novaseqx_47539/RunParameters.xml create mode 100644 t/data/novaseqx_47539/samplesheet_47539.csv diff --git a/MANIFEST b/MANIFEST index f9d13a5d3..8579a0bbf 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1040,6 +1040,10 @@ t/data/novaseq/210415_A00971_0162_AHNNTMDSXY/Data/Intensities/BAM_basecalls_2021 t/data/novaseq/210415_A00971_0162_AHNNTMDSXY/Data/Intensities/BAM_basecalls_20210417-080715/metadata_cache_37416/lane_3.taglist t/data/novaseq/210415_A00971_0162_AHNNTMDSXY/Data/Intensities/BAM_basecalls_20210417-080715/metadata_cache_37416/lane_4.taglist t/data/novaseq/210415_A00971_0162_AHNNTMDSXY/Data/Intensities/BAM_basecalls_20210417-080715/metadata_cache_37416/samplesheet_37416.csv +t/data/novaseqx_47539/README.md +t/data/novaseqx_47539/RunInfo.xml +t/data/novaseqx_47539/RunParameters.xml +t/data/novaseqx_47539/samplesheet_47539.csv t/data/p4_stage1_analysis/1234_samplesheet.csv t/data/p4_stage1_analysis/TileMetricsOut.bin t/data/portable_pipelines/samplesheet4archival_all_controls.csv diff --git a/t/20-function-seq_alignment.t b/t/20-function-seq_alignment.t index 81cf660dd..23f628034 100644 --- a/t/20-function-seq_alignment.t +++ b/t/20-function-seq_alignment.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 19; +use Test::More tests => 20; use Test::Exception; use Test::Deep; use Test::Warn; @@ -1943,4 +1943,111 @@ subtest 'single-end markdup_method test' => sub { } }; +subtest 'test reference caching' => sub { + plan tests => 7; + + my $data_dir = q[t/data/novaseqx_47539]; + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = qq[$data_dir/samplesheet_47539.csv]; + + my $id_run = 47539; + my $runfolder_name = q[20230628_LH00210_0008_B225TGJLT3]; + my $runfolder_path = qq[$dir/20230628_LH00210_0008_B225TGJLT3]; + my $nocal_dir = + qq[$runfolder_path/Data/Intensities/BAM_basecalls_20230914-143003/no_cal]; + my $archive_dir = qq[$nocal_dir/archive]; + + my $lims = st::api::lims->new(id_run => $id_run); + for my $lane ($lims->children) { + my $lane_path = join q[/], $archive_dir, q[lane] . $lane->position; + my @indexes = map {$_->tag_index} $lane->children; + push @indexes, 0, 888; + for my $index (@indexes) { + make_path(join q[/], $lane_path, q[plex] . $index); + } + } + + foreach my $file (qw(RunParameters.xml RunInfo.xml)) { + copy("$data_dir/$file", "$runfolder_path/$file") + } + + # Have to add some references to the test ref repo that was + # created at the beginning of this test file. + my @ref_dirs = qw( + Bordetella_pertussis/Tohama_I/all + Clostridium_difficile/Strain_630/all + Escherichia_coli/K12/all + Escherichia_coli/K12_DH10B/all + Homo_sapiens/GRCh38_15_plus_hs38d1/all + Plasmodium_falciparum/3D7_Jan16v3/all + ); + @ref_dirs = map { "$ref_dir/$_" } @ref_dirs; + + my @ref_names = qw( + B_pertussis_Tahoma_I.fasta + C_difficile_630.fasta + E-coli-K12.fa + CP000948.1.fasta + Homo_sapiens.GRCh38_15_plus_hs38d1.fa + Pf3D7_v3.fa + ); + my @aligners = qw/fasta bwa bwa_mem2 minimap2 picard star/; + + my $i = 0; + while ($i < @ref_dirs) { + my $top_dir = $ref_dirs[$i]; + my $file_name = $ref_names[$i]; + for my $a (@aligners) { + my $dir = join q[/], $top_dir, $a; + make_path($dir); # Create the directory for the reference. + my $path; + if ($a eq 'fasta') { + $path = "$dir/$file_name"; + } elsif ($a eq 'picard') { + my $name = join q[.], $file_name, 'dict'; + $path = "$dir/$name"; + } else { + my $name = join q[.], $file_name, 'do'; # some extension + $path = "$dir/$name"; + } + `touch $path`; # Create the reference file. + } + $i++; + } + + # Need two lanes. One, in which the ref cache miss is recorded + # for a reference for tag zero, and another, where this reference + # is needed for one of the samples. Missing reference results in + # data for tag 2 being unaligned. + + # This test was set up to demonstrate a problem with ref cache + # when a lane preceeding the one where the problem is observed + # has samples with multiple references. The test will start + # passing when the root cause of teh problem is fixed in + # st::api::lims. + my $generator = npg_pipeline::function::seq_alignment->new( + id_run => $id_run, + run_folder => $runfolder_name, + runfolder_path => $runfolder_path, + archive_path => $archive_dir, + repository => $dir, + resource => $default, + conf_path => 't/data/release/config/seq_alignment', + lines => [1, 4], + ); + + lives_ok { $generator->generate() } + 'run seq_alignment function for two lanes'; + + for my $i (qw(1 2)) { + my $json_file = sprintf qq[%s/%i_4#%s_p4s2_pv_in.json], + $nocal_dir, $id_run, $i; + ok (-e $json_file, "File $json_file exists"); + my $p4config = from_json(slurp $json_file); + $p4config = $p4config->{'assign'}->[0]; + is ($p4config->{'rpt'}, '47539_4#' . $i, 'correct rpt key value'); + ok (!exists $p4config->{'no_target_alignment'}, + "the alignment not disabled for tag $i in lane 4"); + } +}; + 1; diff --git a/t/data/novaseqx_47539/README.md b/t/data/novaseqx_47539/README.md new file mode 100644 index 000000000..b03f26e46 --- /dev/null +++ b/t/data/novaseqx_47539/README.md @@ -0,0 +1,7 @@ +Notes for t/data/novaseqx_47539 directory + +A set of files that is sufficient to mock a NovaSeqX run folder +for a real run 47539. Some lanes of this run have multiple +samples with different references. The number of samples in +each lane was reduced to simplify mocking the runfolder and +the reference repository. diff --git a/t/data/novaseqx_47539/RunInfo.xml b/t/data/novaseqx_47539/RunInfo.xml new file mode 100644 index 000000000..0d871966c --- /dev/null +++ b/t/data/novaseqx_47539/RunInfo.xml @@ -0,0 +1,3162 @@ + + + + 225TGJLT3 + LH00210 + 2023-06-28T16:55:32Z + + + + + + + + + + 1_1101 + 1_1102 + 1_1103 + 1_1104 + 1_1105 + 1_1106 + 1_1107 + 1_1108 + 1_1109 + 1_1110 + 1_1111 + 1_1112 + 1_1113 + 1_1114 + 1_1115 + 1_1116 + 1_1117 + 1_1118 + 1_1119 + 1_1120 + 1_1121 + 1_1122 + 1_1123 + 1_1124 + 1_1125 + 1_1126 + 1_1127 + 1_1128 + 1_1129 + 1_1130 + 1_1131 + 1_1132 + 1_1133 + 1_1134 + 1_1135 + 1_1136 + 1_1137 + 1_1138 + 1_1139 + 1_1140 + 1_1141 + 1_1142 + 1_1143 + 1_1144 + 1_1145 + 1_1146 + 1_1147 + 1_1148 + 1_1149 + 1_1150 + 1_1151 + 1_1152 + 1_1153 + 1_1154 + 1_1155 + 1_1156 + 1_1157 + 1_1158 + 1_1159 + 1_1160 + 1_1161 + 1_1162 + 1_1163 + 1_1164 + 1_1165 + 1_1166 + 1_1167 + 1_1168 + 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//nx1-esa.dnapipelines.sanger.ac.uk/staging/IL_seq_data/incoming/20230628_LH00210_0008_B225TGJLT3 + InstrumentPerformance + LocalOrchestrated + LocalAnalysis + NovaSeqXPlus + LH00210 + 20230628_LH00210_0008_B225TGJLT3 + 8 + 10B Sequencing + 10B-01.01.00 + 47539 + NovaSeqXSeries B3 + NovaSeqXSeriesB3 + 1.2345678 + + + 225TGJLT3 + 20750642 + 20080370 + 2024-04-09T00:00:00+01:00 + FlowCell + 10B + + + LC4009058-LC3 + 20740727 + 20066614 + 2024-03-27T00:00:00Z + Reagent + 10B + + + LC2304140485-1 + 23041301 + 20089853 + 2024-07-13T00:00:00+01:00 + Buffer + 10B + + + LC1009924-LC1 + 1000017597 + 20072271 + 2024-04-08T00:00:00+01:00 + SampleTube + 10B + + + LC2007014-LC1 + 17847282 + 20081650 + 2024-02-13T00:00:00Z + Lyo + 10B + + + + + + + + + + + 4.1.7 + + DRAGEN BCL Convert + DRAGEN Germline + DRAGEN Germline + DRAGEN RNA + + + + \ No newline at end of file diff --git a/t/data/novaseqx_47539/samplesheet_47539.csv b/t/data/novaseqx_47539/samplesheet_47539.csv new file mode 100644 index 000000000..69a658748 --- /dev/null +++ b/t/data/novaseqx_47539/samplesheet_47539.csv @@ -0,0 +1,82 @@ +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +1,28479597,RefStds_PCR8021331,,GTTCAAAG,TGCATAAA,,Standard,GTTCAAAG,TGCATAAA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159160,,RefStds_PCR8021331,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +1,28479657,RefStds_PCR8021365,,GTCGCGAC,ACACCTTA,,Standard,GTCGCGAC,ACACCTTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,4159165,,RefStds_PCR8021365,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +1,28479586,RefStds_PCR8021381,,CCAGGTCG,TCACTGGA,,Standard,CCAGGTCG,TCACTGGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,4159167,,RefStds_PCR8021381,,Escherichia_coli (K12),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +1,28479610,RefStds_PCR8021397,,AAGGCCGC,TTTAGACA,,Standard,AAGGCCGC,TTTAGACA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,4159169,,RefStds_PCR8021397,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +1,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +2,28479597,RefStds_PCR8021331,,GTTCAAAG,TGCATAAA,,Standard,GTTCAAAG,TGCATAAA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159160,,RefStds_PCR8021331,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +2,28479609,RefStds_PCR8021333,,TTAACTTA,GTCATCCT,,Standard,TTAACTTA,GTCATCCT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159161,,RefStds_PCR8021333,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +2,28479621,RefStds_PCR8021347,,GCCTAGGG,AGTTGGAG,,Standard,GCCTAGGG,AGTTGGAG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159162,,RefStds_PCR8021347,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +2,28479633,RefStds_PCR8021349,,CGAGGGTT,TGCGCTCA,,Standard,CGAGGGTT,TGCGCTCA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159163,,RefStds_PCR8021349,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,4, +2,28479645,RefStds_PCR8021363,,GAGCGAAC,TGGTAAAG,,Standard,GAGCGAAC,TGGTAAAG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159164,,RefStds_PCR8021363,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,5, +2,28479657,RefStds_PCR8021365,,GTCGCGAC,ACACCTTA,,Standard,GTCGCGAC,ACACCTTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,4159165,,RefStds_PCR8021365,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +2,28479574,RefStds_PCR8021379,,GTCTTGCC,TCTGCCCT,,Standard,GTCTTGCC,TCTGCCCT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159166,,RefStds_PCR8021379,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,7, +2,28479586,RefStds_PCR8021381,,CCAGGTCG,TCACTGGA,,Standard,CCAGGTCG,TCACTGGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,4159167,,RefStds_PCR8021381,,Escherichia_coli (K12),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +2,28479598,RefStds_PCR8021395,,CGTGTGGA,ACCGATTA,,Standard,CGTGTGGA,ACCGATTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159168,,RefStds_PCR8021395,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,9, +2,28479610,RefStds_PCR8021397,,AAGGCCGC,TTTAGACA,,Standard,AAGGCCGC,TTTAGACA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,4159169,,RefStds_PCR8021397,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +2,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +3,66843810,RefStds_PCR-free8023825,,AGTTCAGG,CCAACAGA,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720924,,RefStds_PCR-free8023825,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +3,66843858,RefStds_PCR-free8023829,,CCAAGTCT,AAGGATGA,,HiSeqX PCR free,CCAAGTCT,AAGGATGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,,,,,,8720927,,RefStds_PCR-free8023829,,,,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +3,66843812,RefStds_PCR-free8023841,,ACTAAGAT,AACCGCGG,,HiSeqX PCR free,ACTAAGAT,AACCGCGG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720931,,RefStds_PCR-free8023841,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +3,66843860,RefStds_PCR-free8023845,,CCGTGAAG,CAGTGGAT,,HiSeqX PCR free,CCGTGAAG,CAGTGGAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159410,,RefStds_PCR-free8023845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,4, +3,66843814,RefStds_PCR-free8023857,,ATATGGAT,CTGTATTA,,HiSeqX PCR free,ATATGGAT,CTGTATTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720937,,RefStds_PCR-free8023857,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,5, +3,66843862,RefStds_PCR-free8023861,,ATGGCATG,AAGGTACC,,HiSeqX PCR free,ATGGCATG,AAGGTACC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159412,,RefStds_PCR-free8023861,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +3,66843816,RefStds_PCR-free8023873,,TGCGGCGT,CCTCGGTA,,HiSeqX PCR free,TGCGGCGT,CCTCGGTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720943,,RefStds_PCR-free8023873,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,7, +3,66843864,RefStds_PCR-free8023877,,CGGAACTG,CACTACGA,,HiSeqX PCR free,CGGAACTG,CACTACGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,36329,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Malaria,,,,,4159414,,RefStds_PCR-free8023877,,Plasmodium_falciparum (3D7_Jan16v3),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +3,66843818,RefStds_PCR-free8023889,,CAATTAAC,CGAGATAT,,HiSeqX PCR free,CAATTAAC,CGAGATAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720949,,RefStds_PCR-free8023889,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,9, +3,66843866,RefStds_PCR-free8023893,,TGCGAGAC,CATTGTTG,,HiSeqX PCR free,TGCGAGAC,CATTGTTG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,8720952,,RefStds_PCR-free8023893,,Escherichia_coli (K12_DH10B),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +3,66843820,RefStds_PCR-free8023905,,TATCGCAC,CTTAGTGT,,HiSeqX PCR free,TATCGCAC,CTTAGTGT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,8720956,,RefStds_PCR-free8023905,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,11, +3,66843868,RefStds_PCR-free8023909,,TACTCATA,CCTGTGGC,,HiSeqX PCR free,TACTCATA,CCTGTGGC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,8720960,,RefStds_PCR-free8023909,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,12, +3,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +4,66843810,RefStds_PCR-free8023825,,AGTTCAGG,CCAACAGA,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720924,,RefStds_PCR-free8023825,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +4,66843858,RefStds_PCR-free8023829,,CCAAGTCT,AAGGATGA,,HiSeqX PCR free,CCAAGTCT,AAGGATGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,,,,,,8720927,,RefStds_PCR-free8023829,,,,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +4,66843812,RefStds_PCR-free8023841,,ACTAAGAT,AACCGCGG,,HiSeqX PCR free,ACTAAGAT,AACCGCGG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720931,,RefStds_PCR-free8023841,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +5,66843810,RefStds_PCR-free8023825,,AGTTCAGG,CCAACAGA,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720924,,RefStds_PCR-free8023825,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +5,66843858,RefStds_PCR-free8023829,,CCAAGTCT,AAGGATGA,,HiSeqX PCR free,CCAAGTCT,AAGGATGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,,,,,,8720927,,RefStds_PCR-free8023829,,,,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +5,66843812,RefStds_PCR-free8023841,,ACTAAGAT,AACCGCGG,,HiSeqX PCR free,ACTAAGAT,AACCGCGG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720931,,RefStds_PCR-free8023841,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +5,66843860,RefStds_PCR-free8023845,,CCGTGAAG,CAGTGGAT,,HiSeqX PCR free,CCGTGAAG,CAGTGGAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159410,,RefStds_PCR-free8023845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,4, +5,66843814,RefStds_PCR-free8023857,,ATATGGAT,CTGTATTA,,HiSeqX PCR free,ATATGGAT,CTGTATTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720937,,RefStds_PCR-free8023857,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,5, +5,66843862,RefStds_PCR-free8023861,,ATGGCATG,AAGGTACC,,HiSeqX PCR free,ATGGCATG,AAGGTACC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159412,,RefStds_PCR-free8023861,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +5,66843816,RefStds_PCR-free8023873,,TGCGGCGT,CCTCGGTA,,HiSeqX PCR free,TGCGGCGT,CCTCGGTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720943,,RefStds_PCR-free8023873,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,7, +5,66843864,RefStds_PCR-free8023877,,CGGAACTG,CACTACGA,,HiSeqX PCR free,CGGAACTG,CACTACGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,36329,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Malaria,,,,,4159414,,RefStds_PCR-free8023877,,Plasmodium_falciparum (3D7_Jan16v3),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +5,66843818,RefStds_PCR-free8023889,,CAATTAAC,CGAGATAT,,HiSeqX PCR free,CAATTAAC,CGAGATAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720949,,RefStds_PCR-free8023889,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,9, +5,66843866,RefStds_PCR-free8023893,,TGCGAGAC,CATTGTTG,,HiSeqX PCR free,TGCGAGAC,CATTGTTG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,8720952,,RefStds_PCR-free8023893,,Escherichia_coli (K12_DH10B),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +5,66843820,RefStds_PCR-free8023905,,TATCGCAC,CTTAGTGT,,HiSeqX PCR free,TATCGCAC,CTTAGTGT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,8720956,,RefStds_PCR-free8023905,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,11, +5,66843868,RefStds_PCR-free8023909,,TACTCATA,CCTGTGGC,,HiSeqX PCR free,TACTCATA,CCTGTGGC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,8720960,,RefStds_PCR-free8023909,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,12, +5,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +6,66843810,RefStds_PCR-free8023825,,AGTTCAGG,CCAACAGA,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720924,,RefStds_PCR-free8023825,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +6,66843858,RefStds_PCR-free8023829,,CCAAGTCT,AAGGATGA,,HiSeqX PCR free,CCAAGTCT,AAGGATGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,,,,,,8720927,,RefStds_PCR-free8023829,,,,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +6,66843812,RefStds_PCR-free8023841,,ACTAAGAT,AACCGCGG,,HiSeqX PCR free,ACTAAGAT,AACCGCGG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720931,,RefStds_PCR-free8023841,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +6,66843860,RefStds_PCR-free8023845,,CCGTGAAG,CAGTGGAT,,HiSeqX PCR free,CCGTGAAG,CAGTGGAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159410,,RefStds_PCR-free8023845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,4, +6,66843814,RefStds_PCR-free8023857,,ATATGGAT,CTGTATTA,,HiSeqX PCR free,ATATGGAT,CTGTATTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720937,,RefStds_PCR-free8023857,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,5, +6,66843862,RefStds_PCR-free8023861,,ATGGCATG,AAGGTACC,,HiSeqX PCR free,ATGGCATG,AAGGTACC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159412,,RefStds_PCR-free8023861,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +6,66843816,RefStds_PCR-free8023873,,TGCGGCGT,CCTCGGTA,,HiSeqX PCR free,TGCGGCGT,CCTCGGTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720943,,RefStds_PCR-free8023873,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,7, +6,66843864,RefStds_PCR-free8023877,,CGGAACTG,CACTACGA,,HiSeqX PCR free,CGGAACTG,CACTACGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,36329,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Malaria,,,,,4159414,,RefStds_PCR-free8023877,,Plasmodium_falciparum (3D7_Jan16v3),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +6,66843818,RefStds_PCR-free8023889,,CAATTAAC,CGAGATAT,,HiSeqX PCR free,CAATTAAC,CGAGATAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720949,,RefStds_PCR-free8023889,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,9, +6,66843866,RefStds_PCR-free8023893,,TGCGAGAC,CATTGTTG,,HiSeqX PCR free,TGCGAGAC,CATTGTTG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,8720952,,RefStds_PCR-free8023893,,Escherichia_coli (K12_DH10B),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +6,66843820,RefStds_PCR-free8023905,,TATCGCAC,CTTAGTGT,,HiSeqX PCR free,TATCGCAC,CTTAGTGT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,8720956,,RefStds_PCR-free8023905,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,11, +6,66843868,RefStds_PCR-free8023909,,TACTCATA,CCTGTGGC,,HiSeqX PCR free,TACTCATA,CCTGTGGC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,8720960,,RefStds_PCR-free8023909,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,12, +6,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +7,65828605,EGAN00004178291,,CCGTTAGT,ATCACGAT,,RNA Poly A Globin,CCGTTAGT,ATCACGAT,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178291,,Homo Sapiens,,,,,8511812,,pops212973524,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,1, +7,65828617,EGAN00004178293,,TCGACTCG,TGATCAAA,,RNA Poly A Globin,TCGACTCG,TGATCAAA,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178293,,Homo Sapiens,,,,,8511814,,pops212973526,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,2, +7,65828629,EGAN00004178294,,CGTAAAGA,CGACTTCC,,RNA Poly A Globin,CGTAAAGA,CGACTTCC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178294,,Homo Sapiens,,,,,8511815,,pops212973527,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,3, +7,65828641,EGAN00004178295,,CGTCGTCG,CTCAGAAA,,RNA Poly A Globin,CGTCGTCG,CTCAGAAA,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178295,,Homo Sapiens,,,,,8511816,,pops212973528,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,4, +7,65828653,EGAN00004178297,,TTCTCTTT,TCAGCCTG,,RNA Poly A Globin,TTCTCTTT,TCAGCCTG,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178297,,Homo Sapiens,,,,,8511817,,pops212973529,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,5, +7,65828665,EGAN00004178299,,TCTCATAT,TTTGCACC,,RNA Poly A Globin,TCTCATAT,TTTGCACC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178299,,Homo Sapiens,,,,,8511819,,pops212973531,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,6, +7,65828677,EGAN00004178300,,TCGGGCTG,CGATCTGG,,RNA Poly A Globin,TCGGGCTG,CGATCTGG,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178300,,Homo Sapiens,,,,,8511820,,pops212973532,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,7, +7,65828689,EGAN00004178301,,GGAACGAT,GGCGTCCC,,RNA Poly A Globin,GGAACGAT,GGCGTCCC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178301,,Homo Sapiens,,,,,8511821,,pops212973533,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,8, +7,65828606,EGAN00004178302,,TGTTACAG,GAGCGCGC,,RNA Poly A Globin,TGTTACAG,GAGCGCGC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178302,,Homo Sapiens,,,,,8511823,,pops212973535,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,9, +7,65828618,EGAN00004178304,,TCCACAAA,TGGTGCAC,,RNA Poly A Globin,TCCACAAA,TGGTGCAC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178304,,Homo Sapiens,,,,,8511824,,pops212973536,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,10, +7,65828630,EGAN00004178305,,CGCCTTGA,TGGTGACT,,RNA Poly A Globin,CGCCTTGA,TGGTGACT,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178305,,Homo Sapiens,,,,,8511825,,pops212973537,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,11, +8,65828605,EGAN00004178291,,CCGTTAGT,ATCACGAT,,RNA Poly A Globin,CCGTTAGT,ATCACGAT,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178291,,Homo Sapiens,,,,,8511812,,pops212973524,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,1, +8,65828617,EGAN00004178293,,TCGACTCG,TGATCAAA,,RNA Poly A Globin,TCGACTCG,TGATCAAA,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178293,,Homo Sapiens,,,,,8511814,,pops212973526,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,2, +8,65828629,EGAN00004178294,,CGTAAAGA,CGACTTCC,,RNA Poly A Globin,CGTAAAGA,CGACTTCC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178294,,Homo Sapiens,,,,,8511815,,pops212973527,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,3, +8,65828641,EGAN00004178295,,CGTCGTCG,CTCAGAAA,,RNA Poly A Globin,CGTCGTCG,CTCAGAAA,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178295,,Homo Sapiens,,,,,8511816,,pops212973528,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,4, +8,65828653,EGAN00004178297,,TTCTCTTT,TCAGCCTG,,RNA Poly A Globin,TTCTCTTT,TCAGCCTG,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178297,,Homo Sapiens,,,,,8511817,,pops212973529,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,5, +8,65828665,EGAN00004178299,,TCTCATAT,TTTGCACC,,RNA Poly A Globin,TCTCATAT,TTTGCACC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178299,,Homo Sapiens,,,,,8511819,,pops212973531,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,6, +8,65828677,EGAN00004178300,,TCGGGCTG,CGATCTGG,,RNA Poly A Globin,TCGGGCTG,CGATCTGG,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178300,,Homo Sapiens,,,,,8511820,,pops212973532,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,7, +8,65828689,EGAN00004178301,,GGAACGAT,GGCGTCCC,,RNA Poly A Globin,GGAACGAT,GGCGTCCC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178301,,Homo Sapiens,,,,,8511821,,pops212973533,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,8, +8,65828606,EGAN00004178302,,TGTTACAG,GAGCGCGC,,RNA Poly A Globin,TGTTACAG,GAGCGCGC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178302,,Homo Sapiens,,,,,8511823,,pops212973535,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,9, +8,65828618,EGAN00004178304,,TCCACAAA,TGGTGCAC,,RNA Poly A Globin,TCCACAAA,TGGTGCAC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178304,,Homo Sapiens,,,,,8511824,,pops212973536,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,10, +8,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, From 1ab0c0b5139a3053166b6ac8985fbda2454fe60f Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 1 Nov 2023 11:31:02 +0000 Subject: [PATCH 10/17] Stop wasnings about an undefined value when writing to the log --- lib/npg_pipeline/function/seq_alignment.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/npg_pipeline/function/seq_alignment.pm b/lib/npg_pipeline/function/seq_alignment.pm index 040da7a1b..c537b59b0 100644 --- a/lib/npg_pipeline/function/seq_alignment.pm +++ b/lib/npg_pipeline/function/seq_alignment.pm @@ -237,7 +237,7 @@ sub _alignment_command { ## no critic (Subroutines::ProhibitExcessComplexity) $self->debug(qq{ rpt_list: $rpt_list}); $self->debug(qq{ reference_genome: $reference_genome}); $self->debug(qq{ is_tag_zero_product: $is_tag_zero_product}); - $self->debug(qq{ is_pool: $is_pool}); + $self->debug( q{ is_pool: } . $is_pool ? 1 : 0); $self->debug(qq{ dp_archive_path: $dp_archive_path}); $self->debug(qq{ uses_patterned_flowcell: $uses_patterned_flowcell}); $self->debug(qq{ cache10k_path: $cache10k_path}); From 055f413aaa22dbb6dcaf2231f0946811b0f690e9 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 30 Oct 2023 16:03:39 +0000 Subject: [PATCH 11/17] Added an option to merge by library. --- lib/npg_pipeline/base.pm | 76 +++++++++++++++++++---- lib/npg_pipeline/product/release/irods.pm | 4 +- t/20-function-seq_to_irods_archiver.t | 22 ++++++- 3 files changed, 87 insertions(+), 15 deletions(-) diff --git a/lib/npg_pipeline/base.pm b/lib/npg_pipeline/base.pm index 6ab0ce468..89b41dfe3 100644 --- a/lib/npg_pipeline/base.pm +++ b/lib/npg_pipeline/base.pm @@ -227,6 +227,23 @@ sub _build_merge_lanes { return $self->all_lanes_mergeable; } +=head2 merge_by_library + +=cut + +has q{merge_by_library} => ( + isa => q{Bool}, + is => q{ro}, + lazy_build => 1, + documentation => q{Tells p4 stage2 (seq_alignment) to merge all plexes } . + q{that belong to the same library, except spiked PhiX and }. + q{tag zero)}, +); +sub _build_merge_by_library { + my $self = shift; + return $self->is_indexed && $self->platform_NovaSeqX(); +} + =head2 lims st::api::lims run-level or product-specific object @@ -337,27 +354,62 @@ sub _build_products { my @lane_lims = (); my @data_lims = (); + my @libmerged_data_lims = (); + my $selected_lanes4libmerge = 0; if ($self->has_product_rpt_list) { @data_lims = ($self->lims); } else { my @positions = $self->positions; @lane_lims = map { $self->lims4lane($_) } @positions; + if ($self->merge_lanes) { @data_lims = $self->lims->aggregate_xlanes(@positions); } else { - foreach my $lane (@lane_lims) { - if ($self->is_indexed && $lane->is_pool) { - push @data_lims, $lane->children, $lane->create_tag_zero_object(); - } else { - push @data_lims, $lane; - } + + my %tag0_lims = (); + if ($self->is_indexed) { + %tag0_lims = map { $_->position => $_->create_tag_zero_object() } + grep { $_->is_pool } @lane_lims; + } + + if ($self->merge_by_library) { + + my $all_lims = $self->lims->aggregate_libraries(\@lane_lims); + # Unmerged data, if any, including individual objects for + # spiked controls. + push @data_lims, @{$all_lims->{'single'}}; + # Tag zero LIMS objects for all lanes, merged or unmerged. + push @data_lims, map { $tag0_lims{$_} } (sort keys %tag0_lims); + # Merged data. + @libmerged_data_lims = + map { @{$all_lims->{'merges'}->{$_}} } + ( sort keys %{$all_lims->{'merges'}} ); + # We might be analysing a full set of lanes, but the libraries + # might be merged across some lanes only. + $selected_lanes4libmerge = $self->_selected_lanes || + (!exists $all_lims->{'merges'}->{join q[,], @positions}); + + } else { + # To keep backward-compatible order of pipeline invocations, add + # tag zero LIMS object at the end of other objects for the lane. + @data_lims = map { + exists $tag0_lims{$_->position} ? + ($_->children, $tag0_lims{$_->position}) : $_ + } @lane_lims } } } + my @data_products = map { $self->_lims_object2product($_) } @data_lims; + if (@libmerged_data_lims) { + push @data_products, + map { $self->_lims_object2product($_, $selected_lanes4libmerge) } + @libmerged_data_lims; + } + return { - 'data_products' => [map { $self->_lims_object2product($_) } @data_lims], + 'data_products' => \@data_products, 'lanes' => [map { $self->_lims_object2product($_) } @lane_lims] }; } @@ -365,7 +417,7 @@ sub _build_products { ##### # The boolean flag below defines whether lane numbers are explicitly # listed in directory and file names for merged products. It is set -# to true whenever a subset of all available lanes is analysed. +# to true whenever a subset of all available lanes is analysed. has q{_selected_lanes} => ( isa => q{Bool}, is => q{ro}, @@ -381,13 +433,15 @@ sub _build__selected_lanes { } sub _lims_object2product { - my ($self, $lims) = @_; + my ($self, $lims, $selected_lanes) = @_; + return npg_pipeline::product->new( rpt_list => $lims->rpt_list ? $lims->rpt_list : npg_tracking::glossary::rpt->deflate_rpt($lims), lims => $lims, - selected_lanes => $self->_selected_lanes - ) + selected_lanes => defined $selected_lanes ? + $selected_lanes : $self->_selected_lanes + ); } __PACKAGE__->meta->make_immutable; diff --git a/lib/npg_pipeline/product/release/irods.pm b/lib/npg_pipeline/product/release/irods.pm index 40d295aaf..46a82f837 100644 --- a/lib/npg_pipeline/product/release/irods.pm +++ b/lib/npg_pipeline/product/release/irods.pm @@ -202,8 +202,8 @@ sub irods_product_destination_collection_norf { $run_collection or croak('Run collection iRODS path is required'); $product or croak('Product object is required'); return $per_product_archive - ? join q[/], $run_collection, $product->dir_path() - : $run_collection; + ? join q[/], $run_collection, $product->dir_path($product->selected_lanes) + : $run_collection; } =head2 is_for_irods_release diff --git a/t/20-function-seq_to_irods_archiver.t b/t/20-function-seq_to_irods_archiver.t index 09bf4566a..064a8f5de 100644 --- a/t/20-function-seq_to_irods_archiver.t +++ b/t/20-function-seq_to_irods_archiver.t @@ -291,7 +291,8 @@ subtest 'NovaSeq run' => sub { }; subtest 'NovaSeqX run' => sub { - plan tests => 3, + plan tests => 7, + my $id_run = 47515; my $rf_name = '20230622_LH00210_0007_A225TMTLT3'; my $rfpath_test = abs_path(getcwd) . qq{/t/data/novaseqx/$rf_name}; @@ -319,8 +320,25 @@ subtest 'NovaSeqX run' => sub { my $da = $a->create(); my $d = $da->[0]; like ($d->command, - qr{--collection \S+illumina/runs\S+lane1\/plex1}, + qr{--collection \S+illumina/runs\S+lane1\/plex888}, + 'command has per product iRODS destination collection for spiked in PhiX'); + $d = $da->[8]; + like ($d->command, + qr{--collection \S+illumina/runs\S+lane1\/plex0}, + 'command has per product iRODS destination collection for tag zero'); + $d = $da->[16]; + like ($d->command, + qr{--collection \S+illumina/runs\S+lane1-2-3-4\/plex1}, + 'command has per product iRODS destination collection'); + $d = $da->[21]; + like ($d->command, + qr{--collection \S+illumina/runs\S+lane1-2-3-4\/plex6}, + 'command has per product iRODS destination collection'); + $d = $da->[-1]; + like ($d->command, + qr{--collection \S+illumina/runs\S+lane5-6-7-8\/plex6}, 'command has per product iRODS destination collection'); + }; 1; From bc6baa5186666889a63e9c3799058749f52f5f73 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 16 Nov 2023 16:55:12 +0000 Subject: [PATCH 12/17] Accommodated changes in aggregate_libraries. Accommodated changes in the datastructure returned by st::api::lims->aggregate_libraries(). Simplified the new code. Fixed a bug in the test, which triggered a merge by library, which, in turn, was not possible due to strange LIMS data. --- lib/npg_pipeline/base.pm | 58 +++++++++++++++++------------------ t/20-function-seq_alignment.t | 4 +-- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/lib/npg_pipeline/base.pm b/lib/npg_pipeline/base.pm index 89b41dfe3..0fe98efbf 100644 --- a/lib/npg_pipeline/base.pm +++ b/lib/npg_pipeline/base.pm @@ -10,6 +10,7 @@ use File::Basename; use Readonly; use npg_tracking::glossary::rpt; +use npg_tracking::glossary::composition::factory::rpt_list; use st::api::lims; use npg_pipeline::product; @@ -352,10 +353,7 @@ has q{products} => ( sub _build_products { my $self = shift; - my @lane_lims = (); - my @data_lims = (); - my @libmerged_data_lims = (); - my $selected_lanes4libmerge = 0; + my (@lane_lims, @data_lims); if ($self->has_product_rpt_list) { @data_lims = ($self->lims); @@ -374,42 +372,40 @@ sub _build_products { } if ($self->merge_by_library) { - my $all_lims = $self->lims->aggregate_libraries(\@lane_lims); - # Unmerged data, if any, including individual objects for - # spiked controls. - push @data_lims, @{$all_lims->{'single'}}; + @data_lims = @{$all_lims->{'singles'}}; # Might be empty. # Tag zero LIMS objects for all lanes, merged or unmerged. push @data_lims, map { $tag0_lims{$_} } (sort keys %tag0_lims); - # Merged data. - @libmerged_data_lims = - map { @{$all_lims->{'merges'}->{$_}} } - ( sort keys %{$all_lims->{'merges'}} ); - # We might be analysing a full set of lanes, but the libraries - # might be merged across some lanes only. - $selected_lanes4libmerge = $self->_selected_lanes || - (!exists $all_lims->{'merges'}->{join q[,], @positions}); + + if ( @{$all_lims->{'merges'}} ) { + # If the libraries are merged across a subset of lanes under analysis, + # the 'selected_lanes' flag needs to be flipped to true. + if (!$self->_selected_lanes) { + my $rpt_list = $all_lims->{'merges'}->[0]->rpt_list;; + my $num_components = + npg_tracking::glossary::composition::factory::rpt_list + ->new(rpt_list => $rpt_list) + ->create_composition()->num_components(); + if ($num_components != scalar @lane_lims) { + $self->_set_selected_lanes(1); + } + } + push @data_lims, @{$all_lims->{'merges'}}; + } } else { # To keep backward-compatible order of pipeline invocations, add # tag zero LIMS object at the end of other objects for the lane. @data_lims = map { - exists $tag0_lims{$_->position} ? + exists $tag0_lims{$_->position} ? ($_->children, $tag0_lims{$_->position}) : $_ - } @lane_lims + } @lane_lims; } } } - my @data_products = map { $self->_lims_object2product($_) } @data_lims; - if (@libmerged_data_lims) { - push @data_products, - map { $self->_lims_object2product($_, $selected_lanes4libmerge) } - @libmerged_data_lims; - } - return { - 'data_products' => \@data_products, + 'data_products' => [map { $self->_lims_object2product($_) } @data_lims], 'lanes' => [map { $self->_lims_object2product($_) } @lane_lims] }; } @@ -418,9 +414,12 @@ sub _build_products { # The boolean flag below defines whether lane numbers are explicitly # listed in directory and file names for merged products. It is set # to true whenever a subset of all available lanes is analysed. +# If it is set to false by the builder method, it can be reset to true +# when a full collection of products is constructed. has q{_selected_lanes} => ( isa => q{Bool}, is => q{ro}, + writer => q{_set_selected_lanes}, lazy_build => 1, ); sub _build__selected_lanes { @@ -433,14 +432,13 @@ sub _build__selected_lanes { } sub _lims_object2product { - my ($self, $lims, $selected_lanes) = @_; + my ($self, $lims) = @_; return npg_pipeline::product->new( rpt_list => $lims->rpt_list ? $lims->rpt_list : npg_tracking::glossary::rpt->deflate_rpt($lims), lims => $lims, - selected_lanes => defined $selected_lanes ? - $selected_lanes : $self->_selected_lanes + selected_lanes => $self->_selected_lanes ); } @@ -476,6 +474,8 @@ __END__ =item npg_tracking::glossary::rpt +=item npg_tracking::glossary::composition::factory::rpt_list + =item st::api::lims =item WTSI::DNAP::Utilities::Loggable diff --git a/t/20-function-seq_alignment.t b/t/20-function-seq_alignment.t index 23f628034..ec575c57e 100644 --- a/t/20-function-seq_alignment.t +++ b/t/20-function-seq_alignment.t @@ -2022,7 +2022,7 @@ subtest 'test reference caching' => sub { # This test was set up to demonstrate a problem with ref cache # when a lane preceeding the one where the problem is observed # has samples with multiple references. The test will start - # passing when the root cause of teh problem is fixed in + # passing when the root cause of the problem is fixed in # st::api::lims. my $generator = npg_pipeline::function::seq_alignment->new( id_run => $id_run, @@ -2032,7 +2032,7 @@ subtest 'test reference caching' => sub { repository => $dir, resource => $default, conf_path => 't/data/release/config/seq_alignment', - lines => [1, 4], + lanes => [1, 4], ); lives_ok { $generator->generate() } From c7c7608088bec0504cc991dd42b1cc5ed1d2d460 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 17 Nov 2023 16:29:53 +0000 Subject: [PATCH 13/17] Moved existing NovaSeqX test data. Created t/data/novaseqx directory for all future test runfolders, moved existing test runfolder into this directory. --- MANIFEST | 8 ++++---- t/20-function-seq_alignment.t | 2 +- t/data/{novaseqx_47539 => novaseqx/47539}/README.md | 0 t/data/{novaseqx_47539 => novaseqx/47539}/RunInfo.xml | 0 .../{novaseqx_47539 => novaseqx/47539}/RunParameters.xml | 0 .../47539}/samplesheet_47539.csv | 0 6 files changed, 5 insertions(+), 5 deletions(-) rename t/data/{novaseqx_47539 => novaseqx/47539}/README.md (100%) rename t/data/{novaseqx_47539 => novaseqx/47539}/RunInfo.xml (100%) rename t/data/{novaseqx_47539 => novaseqx/47539}/RunParameters.xml (100%) rename t/data/{novaseqx_47539 => novaseqx/47539}/samplesheet_47539.csv (100%) diff --git a/MANIFEST b/MANIFEST index 8579a0bbf..61595574a 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1040,10 +1040,10 @@ t/data/novaseq/210415_A00971_0162_AHNNTMDSXY/Data/Intensities/BAM_basecalls_2021 t/data/novaseq/210415_A00971_0162_AHNNTMDSXY/Data/Intensities/BAM_basecalls_20210417-080715/metadata_cache_37416/lane_3.taglist t/data/novaseq/210415_A00971_0162_AHNNTMDSXY/Data/Intensities/BAM_basecalls_20210417-080715/metadata_cache_37416/lane_4.taglist t/data/novaseq/210415_A00971_0162_AHNNTMDSXY/Data/Intensities/BAM_basecalls_20210417-080715/metadata_cache_37416/samplesheet_37416.csv -t/data/novaseqx_47539/README.md -t/data/novaseqx_47539/RunInfo.xml -t/data/novaseqx_47539/RunParameters.xml -t/data/novaseqx_47539/samplesheet_47539.csv +t/data/novaseqx/47539/README.md +t/data/novaseqx/47539/RunInfo.xml +t/data/novaseqx/47539/RunParameters.xml +t/data/novaseqx/47539/samplesheet_47539.csv t/data/p4_stage1_analysis/1234_samplesheet.csv t/data/p4_stage1_analysis/TileMetricsOut.bin t/data/portable_pipelines/samplesheet4archival_all_controls.csv diff --git a/t/20-function-seq_alignment.t b/t/20-function-seq_alignment.t index ec575c57e..a0d53a8d3 100644 --- a/t/20-function-seq_alignment.t +++ b/t/20-function-seq_alignment.t @@ -1946,7 +1946,7 @@ subtest 'single-end markdup_method test' => sub { subtest 'test reference caching' => sub { plan tests => 7; - my $data_dir = q[t/data/novaseqx_47539]; + my $data_dir = q[t/data/novaseqx/47539]; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = qq[$data_dir/samplesheet_47539.csv]; my $id_run = 47539; diff --git a/t/data/novaseqx_47539/README.md b/t/data/novaseqx/47539/README.md similarity index 100% rename from t/data/novaseqx_47539/README.md rename to t/data/novaseqx/47539/README.md diff --git a/t/data/novaseqx_47539/RunInfo.xml b/t/data/novaseqx/47539/RunInfo.xml similarity index 100% rename from t/data/novaseqx_47539/RunInfo.xml rename to t/data/novaseqx/47539/RunInfo.xml diff --git a/t/data/novaseqx_47539/RunParameters.xml b/t/data/novaseqx/47539/RunParameters.xml similarity index 100% rename from t/data/novaseqx_47539/RunParameters.xml rename to t/data/novaseqx/47539/RunParameters.xml diff --git a/t/data/novaseqx_47539/samplesheet_47539.csv b/t/data/novaseqx/47539/samplesheet_47539.csv similarity index 100% rename from t/data/novaseqx_47539/samplesheet_47539.csv rename to t/data/novaseqx/47539/samplesheet_47539.csv From 67e1febb606749879ed3b8452a6906a1d617504c Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 17 Nov 2023 16:41:06 +0000 Subject: [PATCH 14/17] Added unit tests for new functionality. --- MANIFEST | 3 + t/10-base.t | 149 +- t/10-runfolder_scaffold.t | 84 +- .../RunInfo.xml | 3162 +++++++++++++++++ .../RunParameters.xml | 69 + .../samplesheet_47995.csv | 184 + 6 files changed, 3641 insertions(+), 10 deletions(-) create mode 100644 t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/RunInfo.xml create mode 100644 t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/RunParameters.xml create mode 100644 t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/samplesheet_47995.csv diff --git a/MANIFEST b/MANIFEST index 61595574a..2d93e029d 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1044,6 +1044,9 @@ t/data/novaseqx/47539/README.md t/data/novaseqx/47539/RunInfo.xml t/data/novaseqx/47539/RunParameters.xml t/data/novaseqx/47539/samplesheet_47539.csv +t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/RunInfo.xml +t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/RunParameters.xml +t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/samplesheet_47995.csv t/data/p4_stage1_analysis/1234_samplesheet.csv t/data/p4_stage1_analysis/TileMetricsOut.bin t/data/portable_pipelines/samplesheet4archival_all_controls.csv diff --git a/t/10-base.t b/t/10-base.t index 9f35ce346..ab83edcc4 100644 --- a/t/10-base.t +++ b/t/10-base.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 8; +use Test::More tests => 9; use Test::Exception; use File::Temp qw(tempdir tempfile); use Cwd; @@ -83,16 +83,20 @@ subtest 'repository preexec' => sub { q{correct ref_adapter_pre_exec_string} ); }; -subtest 'products' => sub { - plan tests => 18; +subtest 'products - merging (or not) lanes' => sub { + plan tests => 19; + + my $rf_path = q[t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3]; + my $b = npg_pipeline::base->new(runfolder_path => $rf_path, id_run => 47995); + ok(!$b->merge_lanes, 'merge by lanes is false for NovaSeqX'); my $rf_info = $util->create_runfolder(); - my $rf_path = $rf_info->{'runfolder_path'}; + $rf_path = $rf_info->{'runfolder_path'}; my $products; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/products/samplesheet_novaseq4lanes.csv'; cp 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; - my $b = npg_pipeline::base->new(runfolder_path => $rf_path, id_run => 999); + $b = npg_pipeline::base->new(runfolder_path => $rf_path, id_run => 999); ok ($b->merge_lanes, 'merge_lanes flag is set'); lives_ok {$products = $b->products} 'products hash created for NovaSeq run'; ok (exists $products->{'lanes'}, 'products lanes key exists'); @@ -123,6 +127,141 @@ subtest 'products' => sub { is (scalar @{$products->{'data_products'}}, 3, 'three data products'); }; +subtest 'products - merging (or not) libraries' => sub { + plan tests => 418; + + my $rf_info = $util->create_runfolder(); + my $rf_path = $rf_info->{'runfolder_path'}; + cp 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; + my $b = npg_pipeline::base->new(runfolder_path => $rf_path, id_run => 999); + ok(!$b->merge_by_library, 'merge by library is false for NovaSeq'); + + $rf_path = q[t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3]; + my $id_run = 47995; + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = qq[$rf_path/samplesheet_${id_run}.csv]; + # All lanes are spiked. Possible merges: + # lanes 1, 2 - 17 samples + # lanes 3, 4 - 10 samples + # lanes 5, 6 - 22 samples + # lanes 7, 8 - 38 samples + $b = npg_pipeline::base->new(runfolder_path => $rf_path, id_run => $id_run); + ok($b->merge_by_library, 'merge by library is true for NovaSeqX'); + my @lane_products = @{$b->products()->{'lanes'}}; + is (@lane_products, 8, 'eight lane products'); + is_deeply ([map { $_->rpt_list } @lane_products], + [map { join q[:], $id_run, $_} (1 .. 8)], + 'lane products have correct rpt lists assigned'); + my @products = @{$b->products()->{'data_products'}}; + is (@products, 103, 'number of data products is 103'); + my @expected = map { join q[:], $id_run, $_, 888 } (1 .. 8); + is_deeply ([map { $_->rpt_list } map { $products[$_] } (0 .. 7)], + \@expected, 'first eight products are for spiked controls'); + @expected = map { join q[:], $id_run, $_, 0 } (1 .. 8); + is_deeply ([map { $_->rpt_list } map { $products[$_] } (8 .. 15)], + \@expected, 'next eight products are for tag zero'); + my $ti = 1; + foreach my $p (map { $products[$_] } (16 .. 32)) { + my $expected_rpt_list = _generate_rpt($id_run, [1,2], $ti); + $ti++; + is ($p->rpt_list, $expected_rpt_list, + "product rpt list $expected_rpt_list as expected"); + ok ($p->selected_lanes, 'selected_lanes flag is set to true'); + } + $ti = 1; + foreach my $p (map { $products[$_] } (33 .. 42)) { + my $expected_rpt_list = _generate_rpt($id_run, [3,4], $ti); + $ti++; + is ($p->rpt_list, $expected_rpt_list, + "product rpt list $expected_rpt_list as expected"); + ok ($p->selected_lanes, 'selected_lanes flag is set to true'); + } + $ti = 1; + foreach my $p (map { $products[$_] } (43 .. 64)) { + my $expected_rpt_list = _generate_rpt($id_run, [5,6], $ti); + $ti++; + is ($p->rpt_list, $expected_rpt_list, + "product rpt list $expected_rpt_list as expected"); + ok ($p->selected_lanes, 'selected_lanes flag is set to true'); + } + $ti = 1; + foreach my $p (map { $products[$_] } (65 .. 102)) { + my $expected_rpt_list = _generate_rpt($id_run, [7,8], $ti); + $ti++; + is ($p->rpt_list, $expected_rpt_list, + "product rpt list $expected_rpt_list as expected"); + ok ($p->selected_lanes, 'selected_lanes flag is set to true'); + } + + # Expect lanes 3 and 4 merged. + $b = npg_pipeline::base->new( + runfolder_path => $rf_path, id_run => $id_run, lanes => [4,8,3]); + ok($b->merge_by_library, 'merge by library is true for NovaSeqX'); + + @lane_products = @{$b->products()->{'lanes'}}; + is (@lane_products, 3, 'three lane products'); + is_deeply ([map { $_->rpt_list } @lane_products], + [map { join q[:], $id_run, $_} (3,4,8)], + 'lane products have correct rpt lists assigned'); + + @products = @{$b->products()->{'data_products'}}; + is (@products, 54, 'number of data products is 54'); + + is ($products[0]->rpt_list, "$id_run:3:888", + 'first single product is for spiked control for lane 3'); + is ($products[1]->rpt_list, "$id_run:4:888", + 'second single product is for spiked control for lane 4'); + # Then all single products for lane 8. + $ti = 1; + foreach my $p (map { $products[$_] } (2 .. 39)) { + my $expected_rpt_list = join q[:], $id_run, 8, $ti; + $ti++; + is ($p->rpt_list, $expected_rpt_list, + "product rpt list $expected_rpt_list as expected"); + ok ($p->selected_lanes, 'selected_lanes flag is set to true'); + } + is ($products[40]->rpt_list, "$id_run:8:888", 'spiked control for lane 8'); + is ($products[41]->rpt_list, "$id_run:3:0", 'tag zero for lane 3'); + is ($products[42]->rpt_list, "$id_run:4:0", 'tag zero for lane 4'); + is ($products[43]->rpt_list, "$id_run:8:0", 'tag zero for lane 8'); + # Then merged data. + $ti = 1; + foreach my $p (map { $products[$_] } (44 .. 53)) { + my $expected_rpt_list = _generate_rpt($id_run, [3,4], $ti); + $ti++; + is ($p->rpt_list, $expected_rpt_list, + "product rpt list $expected_rpt_list as expected"); + ok ($p->selected_lanes, 'selected_lanes flag is set to true'); + } + + # Merge disabled. + $b = npg_pipeline::base->new( + runfolder_path => $rf_path, + id_run => $id_run, + lanes => [4,8,3], + merge_by_library => 0 + ); + ok(!$b->merge_by_library, 'merge by library is false'); + @products = @{$b->products()->{'data_products'}}; + is (@products, 64, 'number of data products is 64'); + + foreach my $position ((3, 4, 8)) { + my $num_plexes = $position == 8 ? 38 : 10; + foreach my $index ((1 .. $num_plexes, 888, 0)) { + my $p = shift @products; + my $expected_rpt_list = join q[:], $id_run, $position, $index; + is ($p->rpt_list, $expected_rpt_list, + "product rpt list $expected_rpt_list as expected"); + ok ($p->selected_lanes, 'selected_lanes flag is set to true'); + } + } + is (@products, 0, 'no products are left'); +}; + +sub _generate_rpt { + my ($id_run, $lanes, $tag_index) = @_; + return join q[;], map { join q[:], $id_run, $_, $tag_index } @{$lanes}; +} + subtest 'label' => sub { plan tests => 4; diff --git a/t/10-runfolder_scaffold.t b/t/10-runfolder_scaffold.t index d69e919a5..47c6c1415 100644 --- a/t/10-runfolder_scaffold.t +++ b/t/10-runfolder_scaffold.t @@ -1,9 +1,11 @@ use strict; use warnings; -use Test::More tests => 5; +use Test::More tests => 6; use Test::Exception; use Moose::Meta::Class; -use File::Copy qw(cp); +use File::Copy::Recursive qw(fcopy dircopy); +use File::Path qw(make_path); + use File::Slurp; use t::util; @@ -70,7 +72,7 @@ subtest 'product level scaffold, NovaSeq all lanes' => sub { my $util = t::util->new(); my $rfh = $util->create_runfolder(); my $rf_path = $rfh->{'runfolder_path'}; - cp 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; + fcopy 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/products/samplesheet_novaseq4lanes.csv'; my $rfs = Moose::Meta::Class->create_anon_class( @@ -122,7 +124,7 @@ subtest 'product level scaffold, NovaSeq selected lanes' => sub { my $util = t::util->new(); my $rfh = $util->create_runfolder(); my $rf_path = $rfh->{'runfolder_path'}; - cp 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; + fcopy 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/products/samplesheet_novaseq4lanes.csv'; my $rfs = Moose::Meta::Class->create_anon_class( @@ -178,4 +180,76 @@ subtest 'product level scaffold, NovaSeq selected lanes' => sub { } }; -1; +subtest 'product level scaffold, library merge for NovaSeqX' => sub { + plan tests => 369; + + my $tdir = t::util->new()->temp_directory(); + my $rf_name = q[20231017_LH00210_0012_B22FCNFLT3]; + my $test_path = qq[t/data/novaseqx/${rf_name}]; + my $rf_path = join q[/], $tdir, $rf_name; + dircopy($test_path, $rf_path); + my $in_path = join q[/], $rf_path, 'Data', 'Intensities'; + make_path($in_path); + my $id_run = 47995; + my $date = '2023'; + my $apath = join q[/], $in_path, "BAM_basecalls_$date", 'no_cal', 'archive'; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = qq[$rf_path/samplesheet_${id_run}.csv]; + + my $rfs = Moose::Meta::Class->create_anon_class( + superclasses => ['npg_pipeline::base'], + roles => [qw/npg_pipeline::runfolder_scaffold/], + )->new_object( + runfolder_path => $rf_path, + timestamp => $date, + id_run => $id_run, + ); + $rfs->create_top_level(); + $rfs->create_product_level(); + + my @lane_dirs = map { 'lane' . $_ } (1 .. 8); + my @dirs = @lane_dirs; + push @dirs, (map {join q[/], $_, 'qc'} @lane_dirs); + push @dirs, (map {join q[/], $_, 'tileviz_'.$_} @lane_dirs); + push @dirs, (map {join q[/], $_, '.npg_cache_10000'} @lane_dirs); + map { ok (-d $_, "$_ created") } map {join q[/], $apath, $_} @dirs; + + # All lanes are spiked. + for my $lane (@lane_dirs) { + for my $t ( (0, 888) ) { + my $plex_dir = join q[/], $apath, $lane, 'plex' . $t; + ok ((-d $plex_dir), "plex directory $plex_dir exists"); + ok ((-d "$plex_dir/qc"), "qc directory for $plex_dir exists"); + ok ((-d "$plex_dir/.npg_cache_10000"), "cache directory for $plex_dir exists"); + } + # Test just a few directories. + for my $t ( (1, 10) ) { + my $plex_dir = join q[/], $apath, $lane, 'plex' . $t; + ok (!(-d $plex_dir), "plex directory $plex_dir does not exist"); + } + } + + my %num_samples_per_merge = ( + '1-2' => 17, + '3-4' => 10, + '5-6' => 22, + '7-8' => 38, + ); + foreach my $merge (keys %num_samples_per_merge) { + my $merge_dir = join q[/], $apath, 'lane' . $merge; + ok ((-d $merge_dir), "$merge_dir exists"); + ok (!(-d "$merge_dir/qc"), + "qc directory for $merge_dir does not exist"); + ok (!(-d "$merge_dir/.npg_cache_10000"), + "cache directory for $merge_dir does not exist"); + foreach my $t ((1 .. $num_samples_per_merge{$merge})) { + my $plex_dir = join q[/], $merge_dir, 'plex' . $t; + ok ((-d $plex_dir), "$plex_dir exists"); + ok ((-d "$plex_dir/qc"), "qc directory for $plex_dir exists"); + ok ((-d "$plex_dir/.npg_cache_10000"), + "cache directory for $plex_dir does not exist"); + } + } +}; + +1; \ No newline at end of file diff --git a/t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/RunInfo.xml b/t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/RunInfo.xml new file mode 100644 index 000000000..be80eac8f --- /dev/null +++ b/t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/RunInfo.xml @@ -0,0 +1,3162 @@ + + + + 22FCNFLT3 + LH00210 + 2023-10-17T17:53:29Z + + + + + + + + + + 1_1101 + 1_1102 + 1_1103 + 1_1104 + 1_1105 + 1_1106 + 1_1107 + 1_1108 + 1_1109 + 1_1110 + 1_1111 + 1_1112 + 1_1113 + 1_1114 + 1_1115 + 1_1116 + 1_1117 + 1_1118 + 1_1119 + 1_1120 + 1_1121 + 1_1122 + 1_1123 + 1_1124 + 1_1125 + 1_1126 + 1_1127 + 1_1128 + 1_1129 + 1_1130 + 1_1131 + 1_1132 + 1_1133 + 1_1134 + 1_1135 + 1_1136 + 1_1137 + 1_1138 + 1_1139 + 1_1140 + 1_1141 + 1_1142 + 1_1143 + 1_1144 + 1_1145 + 1_1146 + 1_1147 + 1_1148 + 1_1149 + 1_1150 + 1_1151 + 1_1152 + 1_1153 + 1_1154 + 1_1155 + 1_1156 + 1_1157 + 1_1158 + 1_1159 + 1_1160 + 1_1161 + 1_1162 + 1_1163 + 1_1164 + 1_1165 + 1_1166 + 1_1167 + 1_1168 + 1_1169 + 1_1170 + 1_1171 + 1_1172 + 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//nx1-esa.dnapipelines.sanger.ac.uk/staging/IL_seq_data/incoming/20231017_LH00210_0012_B22FCNFLT3 + InstrumentPerformance + Manual + None + NovaSeqXPlus + LH00210 + 20231017_LH00210_0012_B22FCNFLT3 + 12 + 10B Sequencing + 10B-01.01.00 + 47995 + NovaSeqXSeries B3 + NovaSeqXSeriesB3 + 1.2345678 + + + 22FCNFLT3 + 20777236 + 20080370 + 2025-01-16T00:00:00Z + FlowCell + 10B + + + LC4039094-LC3 + 20778830 + 20066614 + 2025-02-04T00:00:00Z + Reagent + 10B + + + LC2308030386-1 + 23080201 + 20089853 + 2025-02-02T00:00:00Z + Buffer + 10B + + + LC1023778-LC1 + 1000018756 + 20072271 + 2025-07-25T00:00:00+01:00 + SampleTube + 10B + + + LC2018698-LC1 + 18026054 + 20081650 + 2025-02-04T00:00:00Z + Lyo + 10B + + + + + + + + + + \ No newline at end of file diff --git a/t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/samplesheet_47995.csv b/t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/samplesheet_47995.csv new file mode 100644 index 000000000..e9b167514 --- /dev/null +++ b/t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3/samplesheet_47995.csv @@ -0,0 +1,184 @@ +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +1,65934716,EGAN00004177411,,CCTTCTCT,ATTGAGAG,TE-95148282,Targeted NanoSeq Pulldown Twist,CCTTCTCT,ATTGAGAG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934716,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177411,Normal,Homo sapiens,0,,,PD45703b_tds0003,8508809,0,6751STDY13219549,PD45703b_tds0003,,PD45703b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,1, +1,65934633,EGAN00004177412,,TTTGAGGG,CCCAATCA,TE-95148282,Targeted NanoSeq Pulldown Twist,TTTGAGGG,CCCAATCA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934633,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177412,Normal,Homo sapiens,0,,,PD45704b_tds0002,8508810,0,6751STDY13219550,PD45704b_tds0002,,PD45704b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,2, +1,65934645,EGAN00004177418,,GGCCTGGC,TTGCAATC,TE-95148282,Targeted NanoSeq Pulldown Twist,GGCCTGGC,TTGCAATC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934645,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177418,Normal,Homo sapiens,0,,,PD45704b_tds0003,8508815,0,6751STDY13219555,PD45704b_tds0003,,PD45704b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,3, +1,65934657,EGAN00004177402,,AAAGTGAA,ATGGCAGC,TE-95148282,Targeted NanoSeq Pulldown Twist,AAAGTGAA,ATGGCAGC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934657,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177402,Normal,Homo sapiens,0,,,PD43959b_tds0002,8508801,0,6751STDY13219541,PD43959b_tds0002,,PD43959b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,4, +1,65934669,EGAN00004177414,,ACTCGAAA,CACGCGAC,TE-95148282,Targeted NanoSeq Pulldown Twist,ACTCGAAA,CACGCGAC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934669,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177414,Normal,Homo sapiens,0,,,PD45707b_tds0002,8508812,0,6751STDY13219552,PD45707b_tds0002,,PD45707b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,5, +1,65934681,EGAN00004177417,,CGATTGCA,ACCCAGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,CGATTGCA,ACCCAGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934681,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177417,Normal,Homo sapiens,0,,,PD49159b_tds0002,8508816,0,6751STDY13219556,PD49159b_tds0002,,PD49159b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,6, +1,65934693,EGAN00004177419,,GTAAGCGA,GTTTGGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTAAGCGA,GTTTGGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934693,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177419,Normal,Homo sapiens,0,,,PD49134b_tds0002,8508817,0,6751STDY13219557,PD49134b_tds0002,,PD49134b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,7, +1,65934705,EGAN00004177400,,TTCTTCAG,ACCACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,TTCTTCAG,ACCACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934705,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177400,Normal,Homo sapiens,0,,,PD43957b_tds0002,8508799,0,6751STDY13219539,PD43957b_tds0002,,PD43957b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,8, +1,65934717,EGAN00004177407,,CGTGGATA,TTCCGGTG,TE-95148282,Targeted NanoSeq Pulldown Twist,CGTGGATA,TTCCGGTG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934717,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177407,Normal,Homo sapiens,0,,,PD43958b_tds0002,8508800,0,6751STDY13219540,PD43958b_tds0002,,PD43958b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,9, +1,65934634,EGAN00004177403,,CACTTTGC,AGTCGATG,TE-95148282,Targeted NanoSeq Pulldown Twist,CACTTTGC,AGTCGATG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934634,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177403,Normal,Homo sapiens,0,,,PD43960b_tds0002,8508802,0,6751STDY13219542,PD43960b_tds0002,,PD43960b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,10, +1,65934646,EGAN00004177404,,GTGTCGGT,GATGCGTC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGTCGGT,GATGCGTC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934646,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177404,Normal,Homo sapiens,0,,,PD43961b_tds0002,8508803,0,6751STDY13219543,PD43961b_tds0002,,PD43961b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,11, +1,65934658,EGAN00004177405,,ACGTAACA,ACATTCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,ACGTAACA,ACATTCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934658,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177405,Normal,Homo sapiens,0,,,PD43962b_tds0003,8508804,0,6751STDY13219544,PD43962b_tds0003,,PD43962b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,12, +1,65934670,EGAN00004177406,,CTTTCGAC,CAGACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,CTTTCGAC,CAGACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934670,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177406,Normal,Homo sapiens,0,,,PD43964b_tds0002,8508805,0,6751STDY13219545,PD43964b_tds0002,,PD43964b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,13, +1,65934682,EGAN00004177410,,GTGACCTA,ATAGCGTT,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGACCTA,ATAGCGTT,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934682,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177410,Normal,Homo sapiens,0,,,PD43965b_tds0002,8508806,0,6751STDY13219546,PD43965b_tds0002,,PD43965b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,14, +1,65934694,EGAN00004177408,,GTCCTAAC,TACGCCGA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTCCTAAC,TACGCCGA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934694,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177408,Normal,Homo sapiens,0,,,PD45701b_tds0002,8508807,0,6751STDY13219547,PD45701b_tds0002,,PD45701b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,15, +1,65934706,EGAN00004177413,,GTGCAGGG,AGTCTGCC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGCAGGG,AGTCTGCC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934706,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177413,Normal,Homo sapiens,0,,,PD45705b_tds0002,8508811,0,6751STDY13219551,PD45705b_tds0002,,PD45705b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,16, +1,65934718,EGAN00004177416,,TGCGGTGT,GCAACCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,TGCGGTGT,GCAACCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934718,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177416,Normal,Homo sapiens,0,,,PD49155b_tds0002,8508814,0,6751STDY13219554,PD49155b_tds0002,,PD49155b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,17, +1,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004573,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +2,65934716,EGAN00004177411,,CCTTCTCT,ATTGAGAG,TE-95148282,Targeted NanoSeq Pulldown Twist,CCTTCTCT,ATTGAGAG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934716,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177411,Normal,Homo sapiens,0,,,PD45703b_tds0003,8508809,0,6751STDY13219549,PD45703b_tds0003,,PD45703b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,1, +2,65934633,EGAN00004177412,,TTTGAGGG,CCCAATCA,TE-95148282,Targeted NanoSeq Pulldown Twist,TTTGAGGG,CCCAATCA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934633,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177412,Normal,Homo sapiens,0,,,PD45704b_tds0002,8508810,0,6751STDY13219550,PD45704b_tds0002,,PD45704b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,2, +2,65934645,EGAN00004177418,,GGCCTGGC,TTGCAATC,TE-95148282,Targeted NanoSeq Pulldown Twist,GGCCTGGC,TTGCAATC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934645,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177418,Normal,Homo sapiens,0,,,PD45704b_tds0003,8508815,0,6751STDY13219555,PD45704b_tds0003,,PD45704b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,3, +2,65934657,EGAN00004177402,,AAAGTGAA,ATGGCAGC,TE-95148282,Targeted NanoSeq Pulldown Twist,AAAGTGAA,ATGGCAGC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934657,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177402,Normal,Homo sapiens,0,,,PD43959b_tds0002,8508801,0,6751STDY13219541,PD43959b_tds0002,,PD43959b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,4, +2,65934669,EGAN00004177414,,ACTCGAAA,CACGCGAC,TE-95148282,Targeted NanoSeq Pulldown Twist,ACTCGAAA,CACGCGAC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934669,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177414,Normal,Homo sapiens,0,,,PD45707b_tds0002,8508812,0,6751STDY13219552,PD45707b_tds0002,,PD45707b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,5, +2,65934681,EGAN00004177417,,CGATTGCA,ACCCAGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,CGATTGCA,ACCCAGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934681,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177417,Normal,Homo sapiens,0,,,PD49159b_tds0002,8508816,0,6751STDY13219556,PD49159b_tds0002,,PD49159b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,6, +2,65934693,EGAN00004177419,,GTAAGCGA,GTTTGGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTAAGCGA,GTTTGGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934693,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177419,Normal,Homo sapiens,0,,,PD49134b_tds0002,8508817,0,6751STDY13219557,PD49134b_tds0002,,PD49134b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,7, +2,65934705,EGAN00004177400,,TTCTTCAG,ACCACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,TTCTTCAG,ACCACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934705,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177400,Normal,Homo sapiens,0,,,PD43957b_tds0002,8508799,0,6751STDY13219539,PD43957b_tds0002,,PD43957b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,8, +2,65934717,EGAN00004177407,,CGTGGATA,TTCCGGTG,TE-95148282,Targeted NanoSeq Pulldown Twist,CGTGGATA,TTCCGGTG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934717,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177407,Normal,Homo sapiens,0,,,PD43958b_tds0002,8508800,0,6751STDY13219540,PD43958b_tds0002,,PD43958b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,9, +2,65934634,EGAN00004177403,,CACTTTGC,AGTCGATG,TE-95148282,Targeted NanoSeq Pulldown Twist,CACTTTGC,AGTCGATG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934634,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177403,Normal,Homo sapiens,0,,,PD43960b_tds0002,8508802,0,6751STDY13219542,PD43960b_tds0002,,PD43960b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,10, +2,65934646,EGAN00004177404,,GTGTCGGT,GATGCGTC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGTCGGT,GATGCGTC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934646,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177404,Normal,Homo sapiens,0,,,PD43961b_tds0002,8508803,0,6751STDY13219543,PD43961b_tds0002,,PD43961b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,11, +2,65934658,EGAN00004177405,,ACGTAACA,ACATTCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,ACGTAACA,ACATTCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934658,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177405,Normal,Homo sapiens,0,,,PD43962b_tds0003,8508804,0,6751STDY13219544,PD43962b_tds0003,,PD43962b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,12, +2,65934670,EGAN00004177406,,CTTTCGAC,CAGACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,CTTTCGAC,CAGACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934670,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177406,Normal,Homo sapiens,0,,,PD43964b_tds0002,8508805,0,6751STDY13219545,PD43964b_tds0002,,PD43964b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,13, +2,65934682,EGAN00004177410,,GTGACCTA,ATAGCGTT,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGACCTA,ATAGCGTT,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934682,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177410,Normal,Homo sapiens,0,,,PD43965b_tds0002,8508806,0,6751STDY13219546,PD43965b_tds0002,,PD43965b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,14, +2,65934694,EGAN00004177408,,GTCCTAAC,TACGCCGA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTCCTAAC,TACGCCGA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934694,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177408,Normal,Homo sapiens,0,,,PD45701b_tds0002,8508807,0,6751STDY13219547,PD45701b_tds0002,,PD45701b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,15, +2,65934706,EGAN00004177413,,GTGCAGGG,AGTCTGCC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGCAGGG,AGTCTGCC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934706,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177413,Normal,Homo sapiens,0,,,PD45705b_tds0002,8508811,0,6751STDY13219551,PD45705b_tds0002,,PD45705b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,16, +2,65934718,EGAN00004177416,,TGCGGTGT,GCAACCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,TGCGGTGT,GCAACCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934718,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177416,Normal,Homo sapiens,0,,,PD49155b_tds0002,8508814,0,6751STDY13219554,PD49155b_tds0002,,PD49155b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,17, +2,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004574,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +3,69723082,6050STDY14354621,,TTGATTCC,AGAAGCCC,,Duplex-Seq,TTGATTCC,AGAAGCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723082,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296053,0,6050STDY14354621,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +3,69723083,6050STDY14354622,,CATCATTT,ACCTAACT,,Duplex-Seq,CATCATTT,ACCTAACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723083,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296054,0,6050STDY14354622,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +3,69723084,6050STDY14354623,,ATATGCGC,GCTAATTG,,Duplex-Seq,ATATGCGC,GCTAATTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723084,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296055,0,6050STDY14354623,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +3,69723085,6050STDY14354624,,GTAAATGC,GGTAGGTG,,Duplex-Seq,GTAAATGC,GGTAGGTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723085,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296056,0,6050STDY14354624,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +3,69723086,6050STDY14354625,,TTAGTAGA,AAATTCAC,,Duplex-Seq,TTAGTAGA,AAATTCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723086,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296057,0,6050STDY14354625,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +3,69723087,6050STDY14354626,,CTGATGCT,CTGGATTT,,Duplex-Seq,CTGATGCT,CTGGATTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723087,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296058,0,6050STDY14354626,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +3,69723088,6050STDY14354627,,CTTGCGTG,TACTGCCG,,Duplex-Seq,CTTGCGTG,TACTGCCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723088,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296059,0,6050STDY14354627,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +3,69723089,6050STDY14354628,,CTGTCACA,CATTTATC,,Duplex-Seq,CTGTCACA,CATTTATC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723089,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296060,0,6050STDY14354628,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +3,69723090,6050STDY14354629,,GCCTAGGG,AGTTGGAG,,Duplex-Seq,GCCTAGGG,AGTTGGAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723090,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296061,0,6050STDY14354629,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +3,69723091,6050STDY14354630,,CTTACTCA,TCTCGACC,,Duplex-Seq,CTTACTCA,TCTCGACC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723091,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296062,0,6050STDY14354630,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +3,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004575,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +4,69723082,6050STDY14354621,,TTGATTCC,AGAAGCCC,,Duplex-Seq,TTGATTCC,AGAAGCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723082,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296053,0,6050STDY14354621,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +4,69723083,6050STDY14354622,,CATCATTT,ACCTAACT,,Duplex-Seq,CATCATTT,ACCTAACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723083,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296054,0,6050STDY14354622,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +4,69723084,6050STDY14354623,,ATATGCGC,GCTAATTG,,Duplex-Seq,ATATGCGC,GCTAATTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723084,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296055,0,6050STDY14354623,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +4,69723085,6050STDY14354624,,GTAAATGC,GGTAGGTG,,Duplex-Seq,GTAAATGC,GGTAGGTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723085,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296056,0,6050STDY14354624,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +4,69723086,6050STDY14354625,,TTAGTAGA,AAATTCAC,,Duplex-Seq,TTAGTAGA,AAATTCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723086,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296057,0,6050STDY14354625,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +4,69723087,6050STDY14354626,,CTGATGCT,CTGGATTT,,Duplex-Seq,CTGATGCT,CTGGATTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723087,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296058,0,6050STDY14354626,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +4,69723088,6050STDY14354627,,CTTGCGTG,TACTGCCG,,Duplex-Seq,CTTGCGTG,TACTGCCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723088,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296059,0,6050STDY14354627,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +4,69723089,6050STDY14354628,,CTGTCACA,CATTTATC,,Duplex-Seq,CTGTCACA,CATTTATC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723089,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296060,0,6050STDY14354628,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +4,69723090,6050STDY14354629,,GCCTAGGG,AGTTGGAG,,Duplex-Seq,GCCTAGGG,AGTTGGAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723090,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296061,0,6050STDY14354629,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +4,69723091,6050STDY14354630,,CTTACTCA,TCTCGACC,,Duplex-Seq,CTTACTCA,TCTCGACC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723091,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296062,0,6050STDY14354630,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +4,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004576,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +5,69725419,6050STDY14355627,,CGGAGACA,ATGCGACT,,Duplex-Seq,CGGAGACA,ATGCGACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725419,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296963,0,6050STDY14355627,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +5,69725420,6050STDY14355628,,GTTAACGT,TCACAAAC,,Duplex-Seq,GTTAACGT,TCACAAAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725420,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296964,0,6050STDY14355628,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +5,69725421,6050STDY14355629,,CATTTATT,AGGAGAAA,,Duplex-Seq,CATTTATT,AGGAGAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725421,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296965,0,6050STDY14355629,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +5,69725422,6050STDY14355630,,TTAGCGCA,TCGGCAAA,,Duplex-Seq,TTAGCGCA,TCGGCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725422,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296966,0,6050STDY14355630,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +5,69725423,6050STDY14355631,,TATTCGTA,CTGAAAGA,,Duplex-Seq,TATTCGTA,CTGAAAGA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725423,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296967,0,6050STDY14355631,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_Matched,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +5,69725424,6050STDY14355632,,CTAACTAG,GAAAGGTA,,Duplex-Seq,CTAACTAG,GAAAGGTA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725424,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296968,0,6050STDY14355632,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +5,69725425,6050STDY14355633,,TTTGCAAA,ACACATAT,,Duplex-Seq,TTTGCAAA,ACACATAT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725425,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296969,0,6050STDY14355633,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +5,69725426,6050STDY14355634,,CTTAGAGT,GAACCCTG,,Duplex-Seq,CTTAGAGT,GAACCCTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725426,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296970,0,6050STDY14355634,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +5,69725427,6050STDY14355635,,GGTGGGAA,TAAACCCA,,Duplex-Seq,GGTGGGAA,TAAACCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725427,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296971,0,6050STDY14355635,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +5,69725428,6050STDY14355636,,CCTCCTAA,ATGCACTG,,Duplex-Seq,CCTCCTAA,ATGCACTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725428,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296972,0,6050STDY14355636,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +5,69725429,6050STDY14355637,,TTTCCAGT,ATGCCAAA,,Duplex-Seq,TTTCCAGT,ATGCCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725429,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296973,0,6050STDY14355637,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),11, +5,69725430,6050STDY14355638,,GATATGTG,CCTACTAA,,Duplex-Seq,GATATGTG,CCTACTAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725430,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296974,0,6050STDY14355638,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),12, +5,69725431,6050STDY14355639,,CATGAATC,ATAAACTT,,Duplex-Seq,CATGAATC,ATAAACTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725431,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296975,0,6050STDY14355639,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),13, +5,69725432,6050STDY14355640,,AGTAGTAG,AGGCCGTT,,Duplex-Seq,AGTAGTAG,AGGCCGTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725432,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296976,0,6050STDY14355640,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),14, +5,69725433,6050STDY14355641,,GAGGGCCG,ACCCTCCA,,Duplex-Seq,GAGGGCCG,ACCCTCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725433,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296977,0,6050STDY14355641,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),15, +5,69725434,6050STDY14355642,,TTGTCCAA,CGGATCCC,,Duplex-Seq,TTGTCCAA,CGGATCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725434,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296978,0,6050STDY14355642,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),16, +5,69725435,6050STDY14355643,,CGCAACTG,TGCCATCC,,Duplex-Seq,CGCAACTG,TGCCATCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725435,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296979,0,6050STDY14355643,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),17, +5,69725436,6050STDY14355644,,CATATTCT,CGGACAAG,,Duplex-Seq,CATATTCT,CGGACAAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725436,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296980,0,6050STDY14355644,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_Macthed,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),18, +5,69725437,6050STDY14355645,,GCGGAGAC,CATTGCAC,,Duplex-Seq,GCGGAGAC,CATTGCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725437,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296981,0,6050STDY14355645,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),19, +5,69725438,6050STDY14355646,,TTGGGTGA,ATAAAGCG,,Duplex-Seq,TTGGGTGA,ATAAAGCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725438,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296982,0,6050STDY14355646,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),20, +5,69725439,6050STDY14355647,,GTTCAAAG,TGCATAAA,,Duplex-Seq,GTTCAAAG,TGCATAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725439,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296983,0,6050STDY14355647,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),21, +5,69725440,6050STDY14355648,,TTAACTTA,GTCATCCT,,Duplex-Seq,TTAACTTA,GTCATCCT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725440,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296984,0,6050STDY14355648,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),22, +5,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004577,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +6,69725419,6050STDY14355627,,CGGAGACA,ATGCGACT,,Duplex-Seq,CGGAGACA,ATGCGACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725419,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296963,0,6050STDY14355627,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +6,69725420,6050STDY14355628,,GTTAACGT,TCACAAAC,,Duplex-Seq,GTTAACGT,TCACAAAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725420,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296964,0,6050STDY14355628,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +6,69725421,6050STDY14355629,,CATTTATT,AGGAGAAA,,Duplex-Seq,CATTTATT,AGGAGAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725421,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296965,0,6050STDY14355629,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +6,69725422,6050STDY14355630,,TTAGCGCA,TCGGCAAA,,Duplex-Seq,TTAGCGCA,TCGGCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725422,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296966,0,6050STDY14355630,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +6,69725423,6050STDY14355631,,TATTCGTA,CTGAAAGA,,Duplex-Seq,TATTCGTA,CTGAAAGA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725423,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296967,0,6050STDY14355631,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_Matched,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +6,69725424,6050STDY14355632,,CTAACTAG,GAAAGGTA,,Duplex-Seq,CTAACTAG,GAAAGGTA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725424,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296968,0,6050STDY14355632,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +6,69725425,6050STDY14355633,,TTTGCAAA,ACACATAT,,Duplex-Seq,TTTGCAAA,ACACATAT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725425,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296969,0,6050STDY14355633,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +6,69725426,6050STDY14355634,,CTTAGAGT,GAACCCTG,,Duplex-Seq,CTTAGAGT,GAACCCTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725426,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296970,0,6050STDY14355634,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +6,69725427,6050STDY14355635,,GGTGGGAA,TAAACCCA,,Duplex-Seq,GGTGGGAA,TAAACCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725427,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296971,0,6050STDY14355635,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +6,69725428,6050STDY14355636,,CCTCCTAA,ATGCACTG,,Duplex-Seq,CCTCCTAA,ATGCACTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725428,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296972,0,6050STDY14355636,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +6,69725429,6050STDY14355637,,TTTCCAGT,ATGCCAAA,,Duplex-Seq,TTTCCAGT,ATGCCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725429,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296973,0,6050STDY14355637,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),11, +6,69725430,6050STDY14355638,,GATATGTG,CCTACTAA,,Duplex-Seq,GATATGTG,CCTACTAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725430,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296974,0,6050STDY14355638,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),12, +6,69725431,6050STDY14355639,,CATGAATC,ATAAACTT,,Duplex-Seq,CATGAATC,ATAAACTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725431,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296975,0,6050STDY14355639,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),13, +6,69725432,6050STDY14355640,,AGTAGTAG,AGGCCGTT,,Duplex-Seq,AGTAGTAG,AGGCCGTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725432,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296976,0,6050STDY14355640,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),14, +6,69725433,6050STDY14355641,,GAGGGCCG,ACCCTCCA,,Duplex-Seq,GAGGGCCG,ACCCTCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725433,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296977,0,6050STDY14355641,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),15, +6,69725434,6050STDY14355642,,TTGTCCAA,CGGATCCC,,Duplex-Seq,TTGTCCAA,CGGATCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725434,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296978,0,6050STDY14355642,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),16, +6,69725435,6050STDY14355643,,CGCAACTG,TGCCATCC,,Duplex-Seq,CGCAACTG,TGCCATCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725435,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296979,0,6050STDY14355643,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),17, +6,69725436,6050STDY14355644,,CATATTCT,CGGACAAG,,Duplex-Seq,CATATTCT,CGGACAAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725436,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296980,0,6050STDY14355644,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_Macthed,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),18, +6,69725437,6050STDY14355645,,GCGGAGAC,CATTGCAC,,Duplex-Seq,GCGGAGAC,CATTGCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725437,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296981,0,6050STDY14355645,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),19, +6,69725438,6050STDY14355646,,TTGGGTGA,ATAAAGCG,,Duplex-Seq,TTGGGTGA,ATAAAGCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725438,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296982,0,6050STDY14355646,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),20, +6,69725439,6050STDY14355647,,GTTCAAAG,TGCATAAA,,Duplex-Seq,GTTCAAAG,TGCATAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725439,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296983,0,6050STDY14355647,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),21, +6,69725440,6050STDY14355648,,TTAACTTA,GTCATCCT,,Duplex-Seq,TTAACTTA,GTCATCCT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725440,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296984,0,6050STDY14355648,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),22, +6,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004578,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +7,69510840,EGAN00001321692,,CCGCGGTT,AGCGCTAG,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGCGGTT,AGCGCTAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510840,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321692,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5407888,1497836,,DDD_MAIN5407888,,,DDD_1_FR00569506,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,1, +7,69510852,EGAN00002042187,,TTATAACC,GATATCGA,Twist_Human_Core_Exome_BI,Twist Pulldown,TTATAACC,GATATCGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510852,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042187,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5710659,1823623,,DDD_MAIN5710659,,,DDD_1_FR00569278,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,2, +7,69510864,EGAN00001298465,,GGACTTGG,CGCAGACG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGACTTGG,CGCAGACG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510864,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298465,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5867091,2001421,,DDD_MAIN5867091,,,DDD_1_D500PK129595,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,3, +7,69510876,EGAN00001300772,,AAGTCCAA,TATGAGTA,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGTCCAA,TATGAGTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510876,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300772,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908944,2050909,,DDD_MAIN5908944,,,DDD_1_D500PK129441,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,4, +7,69510888,EGAN00001300773,,ATCCACTG,AGGTGCGT,Twist_Human_Core_Exome_BI,Twist Pulldown,ATCCACTG,AGGTGCGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510888,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300773,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908952,2050917,,DDD_MAIN5908952,,,DDD_1_D500PK129440,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,5, +7,69510900,EGAN00001301174,,GCTTGTCA,GAACATAC,Twist_Human_Core_Exome_BI,Twist Pulldown,GCTTGTCA,GAACATAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510900,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001301174,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5966748,2115694,,DDD_MAIN5966748,,,DDD_1_D500PK128034,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,6, +7,69510924,EGAN00001304327,,TGGATCGA,GTGCGATA,Twist_Human_Core_Exome_BI,Twist Pulldown,TGGATCGA,GTGCGATA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510924,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304327,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6029045,2203893,,DDD_MAIN6029045,,,DDD_1_D0RG141038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,7, +7,69510889,EGAN00001293788,,CCAAGTCT,AAGGATGA,Twist_Human_Core_Exome_BI,Twist Pulldown,CCAAGTCT,AAGGATGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510889,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293788,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5678531,1788223,,DDD_MAIN5678531,,,DDD_1_D575PK144581,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,8, +7,69510901,EGAN00001304217,,TTGGACTC,GGAAGCAG,Twist_Human_Core_Exome_BI,Twist Pulldown,TTGGACTC,GGAAGCAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510901,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304217,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6028474,2203237,,DDD_MAIN6028474,,,DDD_1_FR03967352,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,9, +7,69510913,EGAN00001293786,,GGCTTAAG,TCGTGACC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCTTAAG,TCGTGACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510913,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293786,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670657,1779062,,DDD_MAIN5670657,,,DDD_1_D500PK132121,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,10, +7,69510925,EGAN00001293787,,AATCCGGA,CTACAGTT,Twist_Human_Core_Exome_BI,Twist Pulldown,AATCCGGA,CTACAGTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510925,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293787,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670663,1779068,,DDD_MAIN5670663,,,DDD_1_D500PK132132,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,11, +7,69510842,EGAN00001321167,,TAATACAG,ATATTCAC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAATACAG,ATATTCAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510842,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321167,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5426807,1517975,,DDD_MAIN5426807,,,DDD_1_FR00569436,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,12, +7,69510854,EGAN00002042190,,CGGCGTGA,GCGCCTGT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGCGTGA,GCGCCTGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510854,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042190,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5714029,1828207,,DDD_MAIN5714029,,,DDD_1_FR00559472,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,13, +7,69510866,EGAN00001298517,,ATGTAAGT,ACTCTATG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGTAAGT,ACTCTATG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510866,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298517,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908825,2050790,,DDD_MAIN5908825,,,DDD_1_D575NB050268,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,14, +7,69510878,EGAN00003580492,,GCACGGAC,GTCTCGCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCACGGAC,GTCTCGCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510878,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580492,,Homo Sapiens,0,,,6278STDY12901037,8350874,0,6278STDY12901037,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0086,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,15, +7,69510890,EGAN00003580498,,GGTACCTT,AAGACGTC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGTACCTT,AAGACGTC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510890,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580498,,Homo Sapiens,0,,,6278STDY12901046,8350881,0,6278STDY12901046,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0025,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,16, +7,69510902,EGAN00003580503,,AACGTTCC,GGAGTACT,Twist_Human_Core_Exome_BI,Twist Pulldown,AACGTTCC,GGAGTACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510902,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580503,,Homo Sapiens,0,,,6278STDY12901051,8350885,0,6278STDY12901051,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0529,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,17, +7,69510914,EGAN00003580513,,GCAGAATT,ACCGGCCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCAGAATT,ACCGGCCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510914,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580513,,Homo Sapiens,0,,,6278STDY12901061,8350893,0,6278STDY12901061,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5040,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,18, +7,69510926,EGAN00003580516,,ATGAGGCC,GTTAATTG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGAGGCC,GTTAATTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510926,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580516,,Homo Sapiens,0,,,6278STDY12901069,8350899,0,6278STDY12901069,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5014,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,19, +7,69510843,EGAN00003580522,,ACTAAGAT,AACCGCGG,Twist_Human_Core_Exome_BI,Twist Pulldown,ACTAAGAT,AACCGCGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510843,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580522,,Homo Sapiens,0,,,6278STDY12901078,8350904,0,6278STDY12901078,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5031,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,20, +7,69510855,EGAN00003580559,,GTCGGAGC,GGTTATAA,Twist_Human_Core_Exome_BI,Twist Pulldown,GTCGGAGC,GGTTATAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510855,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580559,,Homo Sapiens,0,,,6278STDY12901100,8350921,0,6278STDY12901100,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_1550,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,21, +7,69510867,EGAN00003580560,,CTTGGTAT,CCAAGTCC,Twist_Human_Core_Exome_BI,Twist Pulldown,CTTGGTAT,CCAAGTCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510867,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580560,,Homo Sapiens,0,,,6278STDY12901101,8350922,0,6278STDY12901101,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,22, +7,69510879,EGAN00003581911,,TCCAACGC,TTGGACTT,Twist_Human_Core_Exome_BI,Twist Pulldown,TCCAACGC,TTGGACTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510879,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581911,,Homo Sapiens,0,,,6278STDY12902768,8352273,0,6278STDY12902768,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0346,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,23, +7,69510891,EGAN00003581913,,CCGTGAAG,CAGTGGAT,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGTGAAG,CAGTGGAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510891,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581913,,Homo Sapiens,0,,,6278STDY12902770,8352275,0,6278STDY12902770,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0324,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,24, +7,69510903,EGAN00003581920,,TTACAGGA,TGACAAGC,Twist_Human_Core_Exome_BI,Twist Pulldown,TTACAGGA,TGACAAGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510903,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581920,,Homo Sapiens,0,,,6278STDY12902777,8352282,0,6278STDY12902777,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0335,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,25, +7,69510915,EGAN00003581923,,GGCATTCT,CTAGCTTG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCATTCT,CTAGCTTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510915,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581923,,Homo Sapiens,0,,,6278STDY12902780,8352285,0,6278STDY12902780,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0301,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,26, +7,69510844,EGAN00003581941,,TACCGAGG,CCTGAACT,Twist_Human_Core_Exome_BI,Twist Pulldown,TACCGAGG,CCTGAACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510844,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581941,,Homo Sapiens,0,,,6278STDY12902798,8352303,0,6278STDY12902798,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0398,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,27, +7,69510868,EGAN00003581945,,AGCCTCAT,AGTAGAGA,Twist_Human_Core_Exome_BI,Twist Pulldown,AGCCTCAT,AGTAGAGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510868,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581945,,Homo Sapiens,0,,,6278STDY12902802,8352307,0,6278STDY12902802,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0383,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,28, +7,69510880,EGAN00003581946,,GATTCTGC,GACGAGAG,Twist_Human_Core_Exome_BI,Twist Pulldown,GATTCTGC,GACGAGAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510880,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581946,,Homo Sapiens,0,,,6278STDY12902803,8352308,0,6278STDY12902803,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0372,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,29, +7,69510892,EGAN00003581951,,TCGTAGTG,AGACTTGG,Twist_Human_Core_Exome_BI,Twist Pulldown,TCGTAGTG,AGACTTGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510892,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581951,,Homo Sapiens,0,,,6278STDY12902808,8352313,0,6278STDY12902808,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0395,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,30, +7,69510904,EGAN00003581955,,CTACGACA,GAGTCCAA,Twist_Human_Core_Exome_BI,Twist Pulldown,CTACGACA,GAGTCCAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510904,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581955,,Homo Sapiens,0,,,6278STDY12902811,8352316,0,6278STDY12902811,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0362,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,31, +7,69510916,EGAN00003581958,,TAAGTGGT,CTTAAGCC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAAGTGGT,CTTAAGCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510916,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581958,,Homo Sapiens,0,,,6278STDY12902815,8352320,0,6278STDY12902815,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0396,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,32, +7,69510928,EGAN00003581970,,CGGACAAC,TCCGGATT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGACAAC,TCCGGATT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510928,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581970,,Homo Sapiens,0,,,6278STDY12902827,8352332,0,6278STDY12902827,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0332,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,33, +7,69510845,EGAN00003581974,,ATATGGAT,CTGTATTA,Twist_Human_Core_Exome_BI,Twist Pulldown,ATATGGAT,CTGTATTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510845,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581974,,Homo Sapiens,0,,,6278STDY12902831,8352336,0,6278STDY12902831,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0376,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,34, +7,69510857,EGAN00003581980,,GCGCAAGC,TCACGCCG,Twist_Human_Core_Exome_BI,Twist Pulldown,GCGCAAGC,TCACGCCG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510857,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581980,,Homo Sapiens,0,,,6278STDY12902837,8352342,0,6278STDY12902837,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0379,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,35, +7,69510869,EGAN00003581983,,AAGATACT,ACTTACAT,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGATACT,ACTTACAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510869,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581983,,Homo Sapiens,0,,,6278STDY12902840,8352345,0,6278STDY12902840,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0355,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,36, +7,69510881,EGAN00003581988,,GGAGCGTC,GTCCGTGC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGAGCGTC,GTCCGTGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510881,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581988,,Homo Sapiens,0,,,6278STDY12902845,8352350,0,6278STDY12902845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0361,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,37, +7,69510893,EGAN00003582081,,ATGGCATG,AAGGTACC,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGGCATG,AAGGTACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510893,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003582081,,Homo Sapiens,0,,,6278STDY12902847,8352352,0,6278STDY12902847,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0368,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,38, +7,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004572,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +8,69510840,EGAN00001321692,,CCGCGGTT,AGCGCTAG,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGCGGTT,AGCGCTAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510840,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321692,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5407888,1497836,,DDD_MAIN5407888,,,DDD_1_FR00569506,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,1, +8,69510852,EGAN00002042187,,TTATAACC,GATATCGA,Twist_Human_Core_Exome_BI,Twist Pulldown,TTATAACC,GATATCGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510852,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042187,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5710659,1823623,,DDD_MAIN5710659,,,DDD_1_FR00569278,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,2, +8,69510864,EGAN00001298465,,GGACTTGG,CGCAGACG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGACTTGG,CGCAGACG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510864,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298465,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5867091,2001421,,DDD_MAIN5867091,,,DDD_1_D500PK129595,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,3, +8,69510876,EGAN00001300772,,AAGTCCAA,TATGAGTA,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGTCCAA,TATGAGTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510876,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300772,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908944,2050909,,DDD_MAIN5908944,,,DDD_1_D500PK129441,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,4, +8,69510888,EGAN00001300773,,ATCCACTG,AGGTGCGT,Twist_Human_Core_Exome_BI,Twist Pulldown,ATCCACTG,AGGTGCGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510888,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300773,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908952,2050917,,DDD_MAIN5908952,,,DDD_1_D500PK129440,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,5, +8,69510900,EGAN00001301174,,GCTTGTCA,GAACATAC,Twist_Human_Core_Exome_BI,Twist Pulldown,GCTTGTCA,GAACATAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510900,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001301174,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5966748,2115694,,DDD_MAIN5966748,,,DDD_1_D500PK128034,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,6, +8,69510924,EGAN00001304327,,TGGATCGA,GTGCGATA,Twist_Human_Core_Exome_BI,Twist Pulldown,TGGATCGA,GTGCGATA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510924,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304327,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6029045,2203893,,DDD_MAIN6029045,,,DDD_1_D0RG141038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,7, +8,69510889,EGAN00001293788,,CCAAGTCT,AAGGATGA,Twist_Human_Core_Exome_BI,Twist Pulldown,CCAAGTCT,AAGGATGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510889,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293788,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5678531,1788223,,DDD_MAIN5678531,,,DDD_1_D575PK144581,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,8, +8,69510901,EGAN00001304217,,TTGGACTC,GGAAGCAG,Twist_Human_Core_Exome_BI,Twist Pulldown,TTGGACTC,GGAAGCAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510901,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304217,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6028474,2203237,,DDD_MAIN6028474,,,DDD_1_FR03967352,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,9, +8,69510913,EGAN00001293786,,GGCTTAAG,TCGTGACC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCTTAAG,TCGTGACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510913,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293786,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670657,1779062,,DDD_MAIN5670657,,,DDD_1_D500PK132121,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,10, +8,69510925,EGAN00001293787,,AATCCGGA,CTACAGTT,Twist_Human_Core_Exome_BI,Twist Pulldown,AATCCGGA,CTACAGTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510925,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293787,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670663,1779068,,DDD_MAIN5670663,,,DDD_1_D500PK132132,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,11, +8,69510842,EGAN00001321167,,TAATACAG,ATATTCAC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAATACAG,ATATTCAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510842,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321167,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5426807,1517975,,DDD_MAIN5426807,,,DDD_1_FR00569436,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,12, +8,69510854,EGAN00002042190,,CGGCGTGA,GCGCCTGT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGCGTGA,GCGCCTGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510854,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042190,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5714029,1828207,,DDD_MAIN5714029,,,DDD_1_FR00559472,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,13, +8,69510866,EGAN00001298517,,ATGTAAGT,ACTCTATG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGTAAGT,ACTCTATG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510866,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298517,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908825,2050790,,DDD_MAIN5908825,,,DDD_1_D575NB050268,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,14, +8,69510878,EGAN00003580492,,GCACGGAC,GTCTCGCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCACGGAC,GTCTCGCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510878,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580492,,Homo Sapiens,0,,,6278STDY12901037,8350874,0,6278STDY12901037,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0086,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,15, +8,69510890,EGAN00003580498,,GGTACCTT,AAGACGTC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGTACCTT,AAGACGTC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510890,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580498,,Homo Sapiens,0,,,6278STDY12901046,8350881,0,6278STDY12901046,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0025,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,16, +8,69510902,EGAN00003580503,,AACGTTCC,GGAGTACT,Twist_Human_Core_Exome_BI,Twist Pulldown,AACGTTCC,GGAGTACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510902,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580503,,Homo Sapiens,0,,,6278STDY12901051,8350885,0,6278STDY12901051,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0529,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,17, +8,69510914,EGAN00003580513,,GCAGAATT,ACCGGCCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCAGAATT,ACCGGCCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510914,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580513,,Homo Sapiens,0,,,6278STDY12901061,8350893,0,6278STDY12901061,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5040,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,18, +8,69510926,EGAN00003580516,,ATGAGGCC,GTTAATTG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGAGGCC,GTTAATTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510926,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580516,,Homo Sapiens,0,,,6278STDY12901069,8350899,0,6278STDY12901069,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5014,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,19, +8,69510843,EGAN00003580522,,ACTAAGAT,AACCGCGG,Twist_Human_Core_Exome_BI,Twist Pulldown,ACTAAGAT,AACCGCGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510843,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580522,,Homo Sapiens,0,,,6278STDY12901078,8350904,0,6278STDY12901078,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5031,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,20, +8,69510855,EGAN00003580559,,GTCGGAGC,GGTTATAA,Twist_Human_Core_Exome_BI,Twist Pulldown,GTCGGAGC,GGTTATAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510855,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580559,,Homo Sapiens,0,,,6278STDY12901100,8350921,0,6278STDY12901100,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_1550,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,21, +8,69510867,EGAN00003580560,,CTTGGTAT,CCAAGTCC,Twist_Human_Core_Exome_BI,Twist Pulldown,CTTGGTAT,CCAAGTCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510867,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580560,,Homo Sapiens,0,,,6278STDY12901101,8350922,0,6278STDY12901101,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,22, +8,69510879,EGAN00003581911,,TCCAACGC,TTGGACTT,Twist_Human_Core_Exome_BI,Twist Pulldown,TCCAACGC,TTGGACTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510879,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581911,,Homo Sapiens,0,,,6278STDY12902768,8352273,0,6278STDY12902768,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0346,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,23, +8,69510891,EGAN00003581913,,CCGTGAAG,CAGTGGAT,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGTGAAG,CAGTGGAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510891,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581913,,Homo Sapiens,0,,,6278STDY12902770,8352275,0,6278STDY12902770,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0324,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,24, +8,69510903,EGAN00003581920,,TTACAGGA,TGACAAGC,Twist_Human_Core_Exome_BI,Twist Pulldown,TTACAGGA,TGACAAGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510903,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581920,,Homo Sapiens,0,,,6278STDY12902777,8352282,0,6278STDY12902777,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0335,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,25, +8,69510915,EGAN00003581923,,GGCATTCT,CTAGCTTG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCATTCT,CTAGCTTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510915,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581923,,Homo Sapiens,0,,,6278STDY12902780,8352285,0,6278STDY12902780,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0301,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,26, +8,69510844,EGAN00003581941,,TACCGAGG,CCTGAACT,Twist_Human_Core_Exome_BI,Twist Pulldown,TACCGAGG,CCTGAACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510844,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581941,,Homo Sapiens,0,,,6278STDY12902798,8352303,0,6278STDY12902798,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0398,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,27, +8,69510868,EGAN00003581945,,AGCCTCAT,AGTAGAGA,Twist_Human_Core_Exome_BI,Twist Pulldown,AGCCTCAT,AGTAGAGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510868,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581945,,Homo Sapiens,0,,,6278STDY12902802,8352307,0,6278STDY12902802,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0383,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,28, +8,69510880,EGAN00003581946,,GATTCTGC,GACGAGAG,Twist_Human_Core_Exome_BI,Twist Pulldown,GATTCTGC,GACGAGAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510880,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581946,,Homo Sapiens,0,,,6278STDY12902803,8352308,0,6278STDY12902803,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0372,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,29, +8,69510892,EGAN00003581951,,TCGTAGTG,AGACTTGG,Twist_Human_Core_Exome_BI,Twist Pulldown,TCGTAGTG,AGACTTGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510892,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581951,,Homo Sapiens,0,,,6278STDY12902808,8352313,0,6278STDY12902808,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0395,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,30, +8,69510904,EGAN00003581955,,CTACGACA,GAGTCCAA,Twist_Human_Core_Exome_BI,Twist Pulldown,CTACGACA,GAGTCCAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510904,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581955,,Homo Sapiens,0,,,6278STDY12902811,8352316,0,6278STDY12902811,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0362,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,31, +8,69510916,EGAN00003581958,,TAAGTGGT,CTTAAGCC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAAGTGGT,CTTAAGCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510916,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581958,,Homo Sapiens,0,,,6278STDY12902815,8352320,0,6278STDY12902815,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0396,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,32, +8,69510928,EGAN00003581970,,CGGACAAC,TCCGGATT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGACAAC,TCCGGATT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510928,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581970,,Homo Sapiens,0,,,6278STDY12902827,8352332,0,6278STDY12902827,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0332,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,33, +8,69510845,EGAN00003581974,,ATATGGAT,CTGTATTA,Twist_Human_Core_Exome_BI,Twist Pulldown,ATATGGAT,CTGTATTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510845,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581974,,Homo Sapiens,0,,,6278STDY12902831,8352336,0,6278STDY12902831,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0376,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,34, +8,69510857,EGAN00003581980,,GCGCAAGC,TCACGCCG,Twist_Human_Core_Exome_BI,Twist Pulldown,GCGCAAGC,TCACGCCG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510857,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581980,,Homo Sapiens,0,,,6278STDY12902837,8352342,0,6278STDY12902837,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0379,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,35, +8,69510869,EGAN00003581983,,AAGATACT,ACTTACAT,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGATACT,ACTTACAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510869,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581983,,Homo Sapiens,0,,,6278STDY12902840,8352345,0,6278STDY12902840,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0355,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,36, +8,69510881,EGAN00003581988,,GGAGCGTC,GTCCGTGC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGAGCGTC,GTCCGTGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510881,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581988,,Homo Sapiens,0,,,6278STDY12902845,8352350,0,6278STDY12902845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0361,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,37, +8,69510893,EGAN00003582081,,ATGGCATG,AAGGTACC,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGGCATG,AAGGTACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510893,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003582081,,Homo Sapiens,0,,,6278STDY12902847,8352352,0,6278STDY12902847,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0368,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,38, +8,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004571,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, From 333db30ebebace30b756300fce3bb5cc35411f8c Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 27 Nov 2023 09:31:59 +0000 Subject: [PATCH 15/17] Recorded the changes --- Changes | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/Changes b/Changes index 375d4eb77..a76f62ffb 100644 --- a/Changes +++ b/Changes @@ -2,6 +2,14 @@ LIST OF CHANGES --------------- - Add in use of autosome target regions for BGE libraries in seq_alignment + - Add 'merge_by_library' pipeline boolean option. This options is automatially + activated for NovaSeqX platform. It triggers a discovery of sets of data + that belong to the same libraries. If cases like this are found, the pipeline + is instructed, at the secondary analysis stage, to process this data as a + single entity. In practice, if the same pool is sequenced in more than one + lane of the run, sample data for the pool are merged across these lanes. + The 'discovery' part of the algorithm is implemented in + https://github.com/wtsi-npg/npg_tracking/pull/772 release 67.0.0 - Turn off spatial filter QC check for NovaSeqX From 8fe4909b0bb6b04ba6397e62cd4d899494a4bbfb Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Mon, 27 Nov 2023 16:21:42 +0000 Subject: [PATCH 16/17] Fix typo in analysis specific overrides for bwa_als_se should map to bwa0_6 and not bw0_6 --- Changes | 1 + lib/npg_pipeline/function/seq_alignment.pm | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/Changes b/Changes index a76f62ffb..114cd83f2 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,7 @@ LIST OF CHANGES --------------- + - Fix typo in analysis specific overrides for bwa_als_se mapping to bwa0_6 - Add in use of autosome target regions for BGE libraries in seq_alignment - Add 'merge_by_library' pipeline boolean option. This options is automatially activated for NovaSeqX platform. It triggers a discovery of sets of data diff --git a/lib/npg_pipeline/function/seq_alignment.pm b/lib/npg_pipeline/function/seq_alignment.pm index 141b9d74a..92a1ae0d0 100644 --- a/lib/npg_pipeline/function/seq_alignment.pm +++ b/lib/npg_pipeline/function/seq_alignment.pm @@ -560,7 +560,7 @@ sub _alignment_command { ## no critic (Subroutines::ProhibitExcessComplexity) ### my $exceptions = { bwa_aln => { aligner => q[bwa0_6], refindex => q[bwa0_6], }, - bwa_aln_se => { aligner => q[bw0_6], refindex => q[bwa0_6], }, + bwa_aln_se => { aligner => q[bwa0_6], refindex => q[bwa0_6], }, bwa_mem => { aligner => q[bwa0_6], refindex => q[bwa0_6], }, bwa_mem_bwakit => { aligner => q[bwa0_6], refindex => q[bwa0_6], }, bwa_mem2 => { aligner => q[bwa-mem2], refindex => q[bwa_mem2], p4_alignment_method => q[bwa_mem] }, From c8b2ab9918f8a772c1d70b1c66644b7b689bee89 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 28 Nov 2023 14:37:36 +0000 Subject: [PATCH 17/17] Updated a list of changes for release 67.1.0 --- Changes | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/Changes b/Changes index 114cd83f2..af13f4727 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,7 @@ LIST OF CHANGES --------------- +release 67.1.0 - Fix typo in analysis specific overrides for bwa_als_se mapping to bwa0_6 - Add in use of autosome target regions for BGE libraries in seq_alignment - Add 'merge_by_library' pipeline boolean option. This options is automatially @@ -11,6 +12,16 @@ LIST OF CHANGES lane of the run, sample data for the pool are merged across these lanes. The 'discovery' part of the algorithm is implemented in https://github.com/wtsi-npg/npg_tracking/pull/772 + - Removed provisions for inline indexes + - Removed a check for rapid runs when deciding whether to merge + - Stop warnings about an undefined value when writing to the log from + npg_pipeline::function::seq_alignment + - Some tests were creating test data in the package's source tree. These + activities are redirected to temporary files and directories in /tmp + - Removed listing of non-existing files from MANIFEST + - Removed superfluous dependency on now removed st::api::request + - Added a test to expose a problem with ref cache, which is resolved by + https://github.com/wtsi-npg/npg_tracking/pull/761 release 67.0.0 - Turn off spatial filter QC check for NovaSeqX