From 05c9c5cdb7e64dd46648a3531d6bdc8347c8d6c4 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Mon, 26 Jun 2023 09:18:20 -0500 Subject: [PATCH 1/3] Update proximal_vcf.rst to mention GATK 3.6.0 --- docs/pvacseq/input_file_prep/proximal_vcf.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/pvacseq/input_file_prep/proximal_vcf.rst b/docs/pvacseq/input_file_prep/proximal_vcf.rst index 2e72c42d9..6ad3c4453 100644 --- a/docs/pvacseq/input_file_prep/proximal_vcf.rst +++ b/docs/pvacseq/input_file_prep/proximal_vcf.rst @@ -110,6 +110,8 @@ ______________________________ Phase variants using GATK’s ReadBackedPhasing _____________________________________________ +Unfortunately, the tool used for this step is no longer available in current versions of GATK. We recommend using GATK 3.6.0 to run this step. + .. code-block:: none /usr/bin/java -Xmx16g -jar /opt/GenomeAnalysisTK.jar \ From f02d7e2e4a372254f59881019940b4d1fb7786b0 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Thu, 27 Jul 2023 14:04:54 +0200 Subject: [PATCH 2/3] Fix some documentation issues --- docs/pvacbind/output_files.rst | 8 ++++---- docs/pvacfuse/output_files.rst | 4 ++-- docs/pvacseq/getting_started.rst | 2 +- docs/pvacseq/output_files.rst | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/pvacbind/output_files.rst b/docs/pvacbind/output_files.rst index 5dd8417f3..5af11239a 100644 --- a/docs/pvacbind/output_files.rst +++ b/docs/pvacbind/output_files.rst @@ -26,11 +26,11 @@ created): * - ``.filtered.tsv`` - The above file after applying all filters, with cleavage site and stability predictions added. - * - ``.filtered.tsv.reference_matches`` (optional) - - A file outlining details of reference proteome matches * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about the best epitope for each mutation in an easy-to-read format. + * - ``.all_epitopes.aggregated.tsv.reference_matches`` (optional) + - A file outlining details of reference proteome matches Filters applied to the filtered.tsv file ---------------------------------------- @@ -243,8 +243,8 @@ Criteria Details .. _pvacbind_reference_matches: -filtered.tsv.reference_matches Report Columns ---------------------------------------------- +aggregated.tsv.reference_matches Report Columns +----------------------------------------------- This file is only generated when the ``--run-reference-proteome-similarity`` option is chosen. diff --git a/docs/pvacfuse/output_files.rst b/docs/pvacfuse/output_files.rst index ba20151ac..ffb93d07e 100644 --- a/docs/pvacfuse/output_files.rst +++ b/docs/pvacfuse/output_files.rst @@ -37,11 +37,11 @@ created): * - ``.filtered.tsv`` - The above file after applying all filters, with cleavage site and stability predictions added. - * - ``.filtered.tsv.reference_matches`` (optional) - - A file outlining details of reference proteome matches * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about the best epitope for each mutation in an easy-to-read format. + * - ``.all_epitopes.aggregated.tsv.reference_matches`` (optional) + - A file outlining details of reference proteome matches Filters applied to the filtered.tsv file ---------------------------------------- diff --git a/docs/pvacseq/getting_started.rst b/docs/pvacseq/getting_started.rst index bc5d737d5..b11a23d8b 100644 --- a/docs/pvacseq/getting_started.rst +++ b/docs/pvacseq/getting_started.rst @@ -12,7 +12,7 @@ The example data output can be reproduced by running the following command: .. code-block:: none pvacseq run \ - /input.vcf \ + /annotated.expression.vcf.gz \ HCC1395_TUMOR_DNA \ HLA-A*29:02,HLA-B*45:01,DRB1*04:05 \ all \ diff --git a/docs/pvacseq/output_files.rst b/docs/pvacseq/output_files.rst index 9786bd7ce..b94321cb0 100644 --- a/docs/pvacseq/output_files.rst +++ b/docs/pvacseq/output_files.rst @@ -41,11 +41,11 @@ created): * - ``.filtered.tsv`` - The above file after applying all filters, with (optionally) cleavage site, stability predictions, and reference proteome similarity metrics added. - * - ``.filtered.tsv.reference_matches`` (optional) - - A file outlining details of reference proteome matches * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about the best epitope for each mutation in an easy-to-read format. + * - ``.all_epitopes.aggregated.tsv.reference_matches`` (optional) + - A file outlining details of reference proteome matches * - ``.all_epitopes.aggregated.metrics.json`` - A JSON file with detailed information about the predicted epitopes, formatted for pVACview. This file, in combination with the From ae35f146c1fc0c2359b87c309d2a5ac2a756b4ac Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Thu, 3 Aug 2023 17:53:07 +0200 Subject: [PATCH 3/3] Add information about missing files for elution-only runs. --- docs/pvacbind/output_files.rst | 5 ++++- docs/pvacfuse/output_files.rst | 5 ++++- docs/pvacseq/output_files.rst | 13 +++++++++---- 3 files changed, 17 insertions(+), 6 deletions(-) diff --git a/docs/pvacbind/output_files.rst b/docs/pvacbind/output_files.rst index 5af11239a..b132d5ec3 100644 --- a/docs/pvacbind/output_files.rst +++ b/docs/pvacbind/output_files.rst @@ -28,7 +28,7 @@ created): predictions added. * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about - the best epitope for each mutation in an easy-to-read format. + the best epitope for each mutation in an easy-to-read format. Not generated when running with elution algorithms only. * - ``.all_epitopes.aggregated.tsv.reference_matches`` (optional) - A file outlining details of reference proteome matches @@ -75,6 +75,9 @@ _______________________________________________ - NetMHCpanEL - NetMHCIIpanEL +Please note that when running pVACfuse with only elution algorithms, no +aggregate report is created. + .. _pvacbind_all_ep_and_filtered: all_epitopes.tsv and filtered.tsv Report Columns diff --git a/docs/pvacfuse/output_files.rst b/docs/pvacfuse/output_files.rst index ffb93d07e..aebcc4494 100644 --- a/docs/pvacfuse/output_files.rst +++ b/docs/pvacfuse/output_files.rst @@ -39,7 +39,7 @@ created): predictions added. * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about - the best epitope for each mutation in an easy-to-read format. + the best epitope for each mutation in an easy-to-read format. Not generated when running with elution algorithms only. * - ``.all_epitopes.aggregated.tsv.reference_matches`` (optional) - A file outlining details of reference proteome matches @@ -89,6 +89,9 @@ _______________________________________________ - NetMHCpanEL - NetMHCIIpanEL +Please note that when running pVACfuse with only elution algorithms, no +aggregate report is created. + all_epitopes.tsv and filtered.tsv Report Columns ------------------------------------------------ diff --git a/docs/pvacseq/output_files.rst b/docs/pvacseq/output_files.rst index b94321cb0..baf12a611 100644 --- a/docs/pvacseq/output_files.rst +++ b/docs/pvacseq/output_files.rst @@ -43,18 +43,20 @@ created): predictions, and reference proteome similarity metrics added. * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about - the best epitope for each mutation in an easy-to-read format. + the best epitope for each mutation in an easy-to-read format. Not + generated when running with elution algorithms only. * - ``.all_epitopes.aggregated.tsv.reference_matches`` (optional) - A file outlining details of reference proteome matches * - ``.all_epitopes.aggregated.metrics.json`` - A JSON file with detailed information about the predicted epitopes, formatted for pVACview. This file, in combination with the aggregated.tsv file, is required to visualize your results - in pVACview. + in pVACview. Not generated when running with elution algorithms only. * - ``ui.R``, ``app.R``, ``server.R``, ``styling.R``, ``anchor_and_helper_functions.R`` - - pVACview R Shiny application files + - pVACview R Shiny application files. Not generated when running with elution algorithms only. * - ``www`` (directory) - - Directory containing image files for pVACview + - Directory containing image files for pVACview. Not generated when running with elution algorithms only. + Filters applied to the filtered.tsv file ---------------------------------------- @@ -101,6 +103,9 @@ _______________________________________________ - NetMHCpanEL - NetMHCIIpanEL +Please note that when running pVACseq with only elution algorithms, no +aggregate report and pVACview files are created. + .. _all_ep_and_filtered: all_epitopes.tsv and filtered.tsv Report Columns