From 1762c9289d52d3ebfd1deb88373ab52da639c0e1 Mon Sep 17 00:00:00 2001 From: Yamato Matsuoka Date: Tue, 28 Nov 2023 19:32:50 -0500 Subject: [PATCH] Add ExpansionHunter, glnexus_cli, lofreq --- bio.json.gz | 4 +- bio.txt | 3 + bio/bash | 2 +- bio/fish | 2 +- bio/json/ExpansionHunter.json | 1 + bio/json/bio.json | 2 +- bio/json/glnexus_cli.json | 1 + bio/json/lofreq.json | 1 + bio/yaml/ExpansionHunter.yaml | 58 +++ bio/yaml/bio.yaml | 11 +- bio/yaml/glnexus_cli.yaml | 55 +++ bio/yaml/lofreq.yaml | 775 ++++++++++++++++++++++++++++++++++ bio/zsh | 2 +- 13 files changed, 908 insertions(+), 9 deletions(-) create mode 100644 bio/json/ExpansionHunter.json create mode 100644 bio/json/glnexus_cli.json create mode 100644 bio/json/lofreq.json create mode 100644 bio/yaml/ExpansionHunter.yaml create mode 100644 bio/yaml/glnexus_cli.yaml create mode 100644 bio/yaml/lofreq.yaml diff --git a/bio.json.gz b/bio.json.gz index 6369ff15..d55de5d3 100644 --- a/bio.json.gz +++ b/bio.json.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:4477d80b47cb8d9f1b2a8601e74d3f827982dd8225b0ec806f084cd9e3c7f97e -size 1035128 +oid sha256:e345439a17d6725f6db11076a6671e2fef4a7b142fb8d367bb796dd22408c60c +size 1039702 diff --git a/bio.txt b/bio.txt index 3ec3c517..1b7c4956 100644 --- a/bio.txt +++ b/bio.txt @@ -1,6 +1,7 @@ Bifrost CrossMap.py DAS_Tool +ExpansionHunter GUESSmyLT Genrich GraphAligner @@ -261,6 +262,7 @@ gfatools gff3-to-ddbj gffread gffutils-cli +glnexus_cli graphlan.py gridss gt @@ -322,6 +324,7 @@ krakenuniq-download load-graph.py load-into-counting.py loadPromoters.pl +lofreq long_fastx lumpy lumpyexpress diff --git a/bio/bash b/bio/bash index 96222396..24c360fd 160000 --- a/bio/bash +++ b/bio/bash @@ -1 +1 @@ -Subproject commit 962223961fc8a7d6a7c6c63d3ea5652e76077299 +Subproject commit 24c360fd76990852427fcb98365b5d4ff63865fb diff --git a/bio/fish b/bio/fish index b73066b6..af00ddb9 160000 --- a/bio/fish +++ b/bio/fish @@ -1 +1 @@ -Subproject commit b73066b6e23f62f635a2cab2040c99dd60345521 +Subproject commit af00ddb9eb3ee9add9548fd6890947a045dc5985 diff --git a/bio/json/ExpansionHunter.json b/bio/json/ExpansionHunter.json new file mode 100644 index 00000000..e79be535 --- /dev/null +++ b/bio/json/ExpansionHunter.json @@ -0,0 +1 @@ +{"name":"ExpansionHunter","description":"A suite of tools for detecting expansions of short tandem repeats","usage":"","options":[{"names":["-h","--help"],"argument":"","description":"Print help message"},{"names":["-v","--version"],"argument":"","description":"Print version number"},{"names":["--reads"],"argument":"arg","description":"BAM/CRAM file with aligned reads"},{"names":["--reference"],"argument":"arg","description":"FASTA file with reference genome"},{"names":["--variant-catalog"],"argument":"arg","description":"JSON file with variants to genotype"},{"names":["--output-prefix"],"argument":"arg","description":"Prefix for the output files"},{"names":["--region-extension-length"],"argument":"arg 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limit"}]},{"name":"mygene","description":"connect to mygene interface","usage":"bio mygene [-h] [-l 5] [-s ''] [-f ''] [-S symbol] [query ...]","options":[{"names":["-h","--help"],"argument":"","description":"show this help message and exit"},{"names":["-l","--limit"],"argument":"5","description":"download limit"},{"names":["-s","--species"],"argument":"''","description":"species"},{"names":["-f","--fields"],"argument":"''","description":"fields"},{"names":["-S","--scopes"],"argument":"symbol","description":"scopes"}]},{"name":"gprofiler","description":"submits genes from a count file to g:Profiler","usage":"bio gprofiler [-h] [-c edger.csv] [-d mmusculus] [-n gene] [-t 0.05] [-p FDR] [-o gprofiler.csv]","options":[{"names":["-h","--help"],"argument":"","description":"show this help message and exit"},{"names":["-c","--counts"],"argument":"edger.csv","description":"input counts"},{"names":["-d","--organism"],"argument":"mmusculus","description":"input counts"},{"names":["-n","--colname"],"argument":"gene","description":"gene id column name"},{"names":["-t","--pval-cutoff"],"argument":"0.05","description":"pvalue cutoff"},{"names":["-p","--pval-column"],"argument":"FDR","description":"pvalue column name"},{"names":["-o","--output"],"argument":"gprofiler.csv","description":"pvalue column name"}]},{"name":"enrichr","description":"submits genes from a count file to Enrichr","usage":"bio enrichr [-h] [-c edger.csv] [-d mmusculus] [-n gene] [-t 0.05] [-p FDR] [-o enrichr.csv]","options":[{"names":["-h","--help"],"argument":"","description":"show this help message and exit"},{"names":["-c","--counts"],"argument":"edger.csv","description":"input counts"},{"names":["-d","--organism"],"argument":"mmusculus","description":"input counts"},{"names":["-n","--colname"],"argument":"gene","description":"gene id column name"},{"names":["-t","--pval-cutoff"],"argument":"0.05","description":"pvalue cutoff"},{"names":["-p","--pval-column"],"argument":"FDR","description":"pvalue column name"},{"names":["-o","--output"],"argument":"enrichr.csv","description":"pvalue column name"}]},{"name":"code","description":"downloads the Biostar Handbook code","usage":"bio code [-h] [-u]","options":[{"names":["-h","--help"],"argument":"","description":"show this help message and exit"},{"names":["-u","--update"],"argument":"","description":"update existing files"}]},{"name":"comm","description":"find common elements","usage":"bio comm [-h] [-1] [-2] [-3] [-t] [-x 1] [-y 1] file1 file2","options":[{"names":["-h","--help"],"argument":"","description":"show this help message and exit"},{"names":["-1","--uniq1"],"argument":"","description":"prints elements unique to file 1"},{"names":["-2","--uniq2"],"argument":"","description":"prints elements unique to file 2"},{"names":["-3","--union"],"argument":"","description":"prints elements present in both files"},{"names":["-t","--tab"],"argument":"","description":"tab delimited (default is csv)"},{"names":["-x","--col1"],"argument":"1","description":"column index for file 1 [default=1]"},{"names":["-y","--col2"],"argument":"1","description":"column index for file 2 [default=1]"}]},{"name":"uniq","description":"find unique elements","usage":"bio uniq [-h] [-f 1] [-c] [-t] [fnames ...]","options":[{"names":["-h","--help"],"argument":"","description":"show this help message and exit"},{"names":["-f","--field"],"argument":"1","description":"field index (1 by default)"},{"names":["-c","--count"],"argument":"","description":"produce counts"},{"names":["-t","--tab"],"argument":"","description":"tab delimited (default is csv)"}]}],"version":"1.6.0","tldr":"> bio is a bioinformatics toy to play with.\n> More information: .\n\n- Fetch genbank data\n\n`bio fetch {{NC_045512}} {{MN996532}} > {{genomes.gb}}`\n\n- Convert the first then bases of the genomes to FASTA.\n\n`bio fasta {{genomes.gb}} --end {{10}}`\n\n- Align the coding sequences for the S protein\n\n`bio fasta {{genomes.gb}} --gene S --protein | bio align | head`\n\n- Print the GFF record that corresponds to the coding sequence for gene S\n\n`bio gff {{genomes.gb}} --gene S`\n\n- Show the descendants of taxid 117565\n\n`bio taxon {{117565}} | head`\n\n- Show the lineage of a taxonomic rank.\n\n`bio taxon {{117565}} --lineage | head`\n\n- Get metadata on a viral sample\n\n`bio meta {{11138}} -H | head`\n"} diff --git a/bio/json/glnexus_cli.json b/bio/json/glnexus_cli.json new file mode 100644 index 00000000..036e4cad --- /dev/null +++ b/bio/json/glnexus_cli.json @@ -0,0 +1 @@ +{"name":"glnexus_cli","description":"Merge and joint-call input gVCF files, emitting multi-sample BCF on standard output","usage":"glnexus_cli [options] /vcf/file/1 .. /vcf/file/N","options":[{"names":["--dir","-d"],"argument":"DIR","description":"scratch directory path (mustn't already exist; default: ./GLnexus.DB)"},{"names":["--config","-c"],"argument":"X","description":"configuration preset name or .yml filename (default: gatk)"},{"names":["--bed","-b"],"argument":"FILE","description":"three-column BED file with ranges to analyze (if neither --range nor --bed: use full length of all contigs)"},{"names":["--list","-l"],"argument":"","description":"expect given files to contain lists of gVCF filenames, one per line"},{"names":["--more-PL","-P"],"argument":"","description":"include PL from reference bands and other cases omitted by default"},{"names":["--squeeze","-S"],"argument":"","description":"reduce pVCF size by suppressing detail in cells derived from reference bands"},{"names":["--trim-uncalled-alleles","-a"],"argument":"","description":"remove alleles with no output GT calls in postprocessing"},{"names":["--mem-gbytes","-m"],"argument":"X","description":"memory budget, in gbytes (default: most of system memory)"},{"names":["--threads","-t"],"argument":"X","description":"thread budget (default: all hardware threads)"},{"names":["--help","-h"],"argument":"","description":"print this help message"}],"version":"v1.4.1-0-g68e25e5"} diff --git a/bio/json/lofreq.json b/bio/json/lofreq.json new file mode 100644 index 00000000..361d76ad --- /dev/null +++ b/bio/json/lofreq.json @@ -0,0 +1 @@ +{"name":"lofreq","description":"Fast and sensitive inference of SNVs and indels","usage":"lofreq [options]","options":[],"subcommands":[{"name":"call","description":"Call variants","usage":"lofreq call [options] in.bam","options":[{"names":["-f","--ref"],"argument":"FILE","description":"Indexed reference fasta file (gzip supported) [null]"},{"names":["-o","--out"],"argument":"FILE","description":"Vcf output file [- = stdout]"},{"names":["-r","--region"],"argument":"STR","description":"Limit calls to this region (chrom:start-end) [null]"},{"names":["-l","--bed"],"argument":"FILE","description":"List of 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(BAQ)"},{"names":["-A","--no-idaq"],"argument":"","description":"Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)"},{"names":["-D","--del-baq"],"argument":"","description":"Delete pre-existing BAQ values, i.e. compute even if already present in BAM"},{"names":["-e","--no-ext-baq"],"argument":"","description":"Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)"},{"names":["-m","--min-mq"],"argument":"INT","description":"Skip reads with mapping quality smaller than INT [0]"},{"names":["-M","--max-mq"],"argument":"INT","description":"Cap mapping quality at INT [255]"},{"names":["-N","--no-mq"],"argument":"","description":"Don't merge mapping quality in LoFreq's model"},{"names":["--call-indels"],"argument":"","description":"Enable indel calls (note: preprocess your file to include indel alignment qualities!)"},{"names":["--only-indels"],"argument":"","description":"Only call indels; no 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Multiple files can be given separated by commas"},{"names":["-T","--def-nm-q"],"argument":"INT","description":"If >= 0, then replace non-match base qualities with this default value [-1]"},{"names":["-a","--sig"],"argument":"","description":"P-Value cutoff / significance level [0.010000]"},{"names":["-b","--bonf"],"argument":"","description":"Bonferroni factor. 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Just output pileup summary per column"},{"names":["--no-default-filter"],"argument":"","description":"Don't run default 'lofreq filter' automatically after calling variants"},{"names":["--force-overwrite"],"argument":"","description":"Overwrite any existing output"},{"names":["--verbose"],"argument":"","description":"Be verbose"},{"names":["--debug"],"argument":"","description":"Enable debugging"}]},{"name":"call-parallel","description":"Call variants in parallel","usage":"","options":[]},{"name":"somatic","description":"Call somatic variants","usage":"lofreq somatic [-h] [-v] -n NORMAL -t TUMOR -o OUTPREFIX -f REF [-l BED] [-d DBSNP] [--threads NUM_THREADS] [--tumor-mtc {bonf,holm-bonf,fdr}] [--tumor-mtc-alpha TUMOR_MTC_ALPHA] [--indel-tumor-mtc {bonf,holm-bonf,fdr}] [--indel-tumor-mtc-alpha INDEL_TUMOR_MTC_ALPHA] [--call-indels] [--min-cov MIN_COV] [--germline] [-S IGN_VCF] [--use-orphan] [--baq-off] [--call-rlx-extra-args CALL_RLX_EXTRA_ARGS] [--no-src-qual] [--debug] [--continue]","options":[{"names":["-h","--help"],"argument":"","description":"show this help message and exit"},{"names":["-v","--verbose"],"argument":"","description":"Be verbose"},{"names":["-n","--normal"],"argument":"NORMAL","description":"Normal BAM file"},{"names":["-t","--tumor"],"argument":"TUMOR","description":"Tumor BAM file"},{"names":["-o","--outprefix"],"argument":"OUTPREFIX","description":"Prefix for output files"},{"names":["-f","--ref"],"argument":"REF","description":"Reference fasta file"},{"names":["-l","--bed"],"argument":"BED","description":"BED file listing regions to restrict analysis to"},{"names":["-d","--dbsnp"],"argument":"DBSNP","description":"vcf-file (bgzipped and index with tabix) containing known germline variants (e.g. dbsnp for human"},{"names":["--threads"],"argument":"NUM_THREADS","description":"Use this many threads for each call"},{"names":["--tumor-mtc"],"argument":"{bonf,holm-bonf,fdr}","description":"Type of multiple testing correction for tumor (default: bonf)"},{"names":["--tumor-mtc-alpha"],"argument":"TUMOR_MTC_ALPHA","description":"Multiple testing correction alpha for tumor (default: 1.000000)"},{"names":["--indel-tumor-mtc"],"argument":"{bonf,holm-bonf,fdr}","description":"Type of multiple testing correction for tumor (default: bonf)"},{"names":["--indel-tumor-mtc-alpha"],"argument":"INDEL_TUMOR_MTC_ALPHA","description":"Multiple testing correction alpha for tumor (default: 0.010000)"},{"names":["--call-indels"],"argument":"","description":"Also call indels (see documentation on how to preprocess your BAM files)"},{"names":["--min-cov"],"argument":"MIN_COV","description":"Minimum coverage for somatic calls (default: 7)"},{"names":["--germline"],"argument":"","description":"Also list germline calls in separate file"},{"names":["-S","--ign-vcf"],"argument":"IGN_VCF","description":"Ignore variants in this vcf-file for source quality computation in tumor (collides with --no-src-qual). 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Default (=-1) is to use median quality of bases in read."},{"names":["-o","--out"],"argument":"FILE","description":"Output BAM file [- = stdout = default]"},{"names":["--verbose"],"argument":"","description":"Be verbose"}]},{"name":"indelqual","description":"Insert indel qualities","usage":"lofreq indelqual [options] in.bam","options":[{"names":["-u","--uniform"],"argument":"INT[,INT]","description":"Add this indel quality uniformly to all bases. Use two comma separated values to specify insertion and deletion quality separately. 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Conflicts with -b."},{"names":["-b","--sb-mtc"],"argument":"STRING","description":"Multiple testing correction type. One of 'bonf', 'holm' or 'fdr'. Conflicts with -B"},{"names":["-c","--sb-alpha"],"argument":"FLOAT","description":"Multiple testing correction pvalue threshold"},{"names":["--sb-no-compound"],"argument":"","description":"Don't use compound filter"},{"names":["--sb-incl-indels"],"argument":"","description":"Apply SB filter to indels as well"},{"names":["-Q","--snvqual-thresh"],"argument":"INT","description":"Minimum phred-value allowed. Conflicts with -q"},{"names":["-q","--snvqual-mtc"],"argument":"STRING","description":"Multiple testing correction type. One of 'bonf', 'holm' or 'fdr'. Conflicts with -Q"},{"names":["-r","--snvqual-alpha"],"argument":"FLOAT","description":"Multiple testing correction pvalue threshold"},{"names":["-s","--snvqual-ntests"],"argument":"INT","description":"Number of performed SNV tests for multiple testing correction"},{"names":["-K","--indelqual-thresh"],"argument":"INT","description":"Minimum phred-value allowed. Conflicts with -q"},{"names":["-k","--indelqual-mtc"],"argument":"STRING","description":"Multiple testing correction type. One of 'bonf', 'holm' or 'fdr'. Conflicts with -Q"},{"names":["-l","--indelqual-alpha"],"argument":"FLOAT","description":"Multiple testing correction pvalue threshold"},{"names":["-m","--indelqual-ntests"],"argument":"INT","description":"Number of performed indel tests for multiple testing correction"},{"names":["--only-indels"],"argument":"","description":"Keep InDels only"},{"names":["--only-snvs"],"argument":"","description":"Keep SNVs only"},{"names":["--print-all"],"argument":"","description":"Print all, not just passed variants"},{"names":["--no-defaults"],"argument":"","description":"Remove all default filter settings"},{"names":["--verbose"],"argument":"","description":"Be verbose"},{"names":["--debug"],"argument":"","description":"Enable debugging"}]},{"name":"uniq","description":"Test whether variants predicted in only one sample really are unique","usage":"lofreq uniq [options] indexed-in.bam","options":[{"names":["-v","--vcf-in"],"argument":"FILE","description":"Input vcf file listing variants [- = stdin; gzip supported]"},{"names":["-o","--vcf-out"],"argument":"FILE","description":"Output vcf file [- = stdout; gzip supported]"},{"names":["-f","--uni-freq"],"argument":"","description":"Assume variants have uniform test frequency of this value (unused if <=0) [-1.000000]"},{"names":["-t","--uniq-thresh"],"argument":"INT","description":"Minimum uniq phred-value required. Conflicts with -m. 0 for off (default=0)"},{"names":["-m","--uniq-mtc"],"argument":"STRING","description":"Uniq multiple testing correction type. One of 'bonf', 'holm' or 'fdr'. (default=MTC_FDR)"},{"names":["-a","--uniq-alpha"],"argument":"FLOAT","description":"Uniq Multiple testing correction p-value threshold (default=0.001000)"},{"names":["-n","--uniq-ntests"],"argument":"INT","description":"Uniq multiple testing correction p-value threshold (default=#vars)"},{"names":["--output-all"],"argument":"","description":"Report all variants instead of only the ones, marked unique. Note, that variants already filtered in input will not be printed."},{"names":["--use-det-lim"],"argument":"","description":"Report variants if they are above implied detection limit Default is to use binomial test to check for frequency differences"},{"names":["--use-orphan"],"argument":"","description":"Don't ignore anomalous read pairs / orphan reads"},{"names":["--verbose"],"argument":"","description":"Be verbose"},{"names":["--debug"],"argument":"","description":"Enable debugging"}]},{"name":"plpsummary","description":"Print pileup summary per position","usage":"lofreq call [options] in.bam","options":[{"names":["-f","--ref"],"argument":"FILE","description":"Indexed reference fasta file (gzip supported) [null]"},{"names":["-o","--out"],"argument":"FILE","description":"Vcf output file [- = stdout]"},{"names":["-r","--region"],"argument":"STR","description":"Limit calls to this region (chrom:start-end) [null]"},{"names":["-l","--bed"],"argument":"FILE","description":"List of positions (chr pos) or regions (BED) [null]"},{"names":["-q","--min-bq"],"argument":"INT","description":"Skip any base with baseQ smaller than INT [6]"},{"names":["-Q","--min-alt-bq"],"argument":"INT","description":"Skip alternate bases with baseQ smaller than INT [6]"},{"names":["-R","--def-alt-bq"],"argument":"INT","description":"Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0]"},{"names":["-j","--min-jq"],"argument":"INT","description":"Skip any base with joinedQ smaller than INT [0]"},{"names":["-J","--min-alt-jq"],"argument":"INT","description":"Skip alternate bases with joinedQ smaller than INT [0]"},{"names":["-K","--def-alt-jq"],"argument":"INT","description":"Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0]"},{"names":["-B","--no-baq"],"argument":"","description":"Disable use of base-alignment quality (BAQ)"},{"names":["-A","--no-idaq"],"argument":"","description":"Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)"},{"names":["-D","--del-baq"],"argument":"","description":"Delete pre-existing BAQ values, i.e. compute even if already present in BAM"},{"names":["-e","--no-ext-baq"],"argument":"","description":"Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)"},{"names":["-m","--min-mq"],"argument":"INT","description":"Skip reads with mapping quality smaller than INT [0]"},{"names":["-M","--max-mq"],"argument":"INT","description":"Cap mapping quality at INT [255]"},{"names":["-N","--no-mq"],"argument":"","description":"Don't merge mapping quality in LoFreq's model"},{"names":["--call-indels"],"argument":"","description":"Enable indel calls (note: preprocess your file to include indel alignment qualities!)"},{"names":["--only-indels"],"argument":"","description":"Only call indels; no SNVs"},{"names":["-s","--src-qual"],"argument":"","description":"Enable computation of source quality"},{"names":["-S","--ign-vcf"],"argument":"FILE","description":"Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas"},{"names":["-T","--def-nm-q"],"argument":"INT","description":"If >= 0, then replace non-match base qualities with this default value [-1]"},{"names":["-a","--sig"],"argument":"","description":"P-Value cutoff / significance level [0.010000]"},{"names":["-b","--bonf"],"argument":"","description":"Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']"},{"names":["-C","--min-cov"],"argument":"INT","description":"Test only positions having at least this coverage [1] (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)"},{"names":["-d","--max-depth"],"argument":"INT","description":"Cap coverage at this depth [1000000]"},{"names":["--illumina-1.3"],"argument":"","description":"Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded"},{"names":["--use-orphan"],"argument":"","description":"Count anomalous read pairs (i.e. where mate is not aligned properly)"},{"names":["--plp-summary-only"],"argument":"","description":"No variant calling. Just output pileup summary per column"},{"names":["--no-default-filter"],"argument":"","description":"Don't run default 'lofreq filter' automatically after calling variants"},{"names":["--force-overwrite"],"argument":"","description":"Overwrite any existing output"},{"names":["--verbose"],"argument":"","description":"Be verbose"},{"names":["--debug"],"argument":"","description":"Enable debugging"}]},{"name":"vcfset","description":"VCF set operations","usage":"lofreq vcfset [options] -a op -1 1.vcf -2 2.vcf","options":[{"names":["-1","--vcf1"],"argument":"FILE","description":"1st VCF input file (bgzip supported)"},{"names":["-2","--vcf2"],"argument":"FILE","description":"2nd VCF input file (mandatory - except for concat - and needs to be tabix indexed)"},{"names":["-o","--vcfout"],"argument":"","description":"VCF output file (default: - for stdout; gzip supported)."},{"names":["-a","--action"],"argument":"","description":"Set operation to perform: intersect, complement or concat. - intersect = vcf1 AND vcf2. - complement = vcf1 \\ vcf2. - concat = vcf1 + vcf2 ... vcfn (output as in file order, i.e. output not necessarily sorted!)"},{"names":["-I","--add-info"],"argument":"STR","description":"Add info field, e.g. 'SOMATIC'"},{"names":["--count-only"],"argument":"","description":"Don't print bases, just numbers"},{"names":["--only-pos"],"argument":"","description":"Disable allele-awareness by using position only (ignoring bases) as key for storing and comparison"},{"names":["--only-passed"],"argument":"","description":"Ignore variants marked as filtered"},{"names":["--only-snvs"],"argument":"","description":"Ignore anything but SNVs in both input files"},{"names":["--only-indels"],"argument":"","description":"Ignore anything but indels in both input files"},{"names":["--verbose"],"argument":"","description":"Be verbose"},{"names":["--debug"],"argument":"","description":"Enable debugging"}]},{"name":"version","description":"Print version info","usage":"","options":[]},{"name":"idxstats","description":"Print stats for indexed BAM file","usage":"samtools idxstats ","options":[]},{"name":"vcfplot","description":"Plot VCF statistics","usage":"","options":[]}],"version":"version: 2.1.5"} diff --git a/bio/yaml/ExpansionHunter.yaml b/bio/yaml/ExpansionHunter.yaml new file mode 100644 index 00000000..f33de945 --- /dev/null +++ b/bio/yaml/ExpansionHunter.yaml @@ -0,0 +1,58 @@ +name: ExpansionHunter +description: A suite of tools for detecting expansions of short tandem repeats +usage: "" +options: + - names: + - -h + - --help + argument: "" + description: Print help message + - names: + - -v + - --version + argument: "" + description: Print version number + - names: + - --reads + argument: arg + description: BAM/CRAM file with aligned reads + - names: + - --reference + argument: arg + description: FASTA file with reference genome + - names: + - --variant-catalog + argument: arg + description: JSON file with variants to genotype + - names: + - --output-prefix + argument: arg + description: Prefix for the output files + - names: + - --region-extension-length + argument: arg (=1000) + description: How far from on/off-target regions to search for informative reads + - names: + - --sex + argument: arg (=female) + description: Sex of the sample; must be either male or female + - names: + - --log-level + argument: arg (=info) + description: trace, debug, info, warn, or error + - names: + - -a + - --aligner + argument: arg (=dag-aligner) + description: Specify which aligner to use (dag-aligner or path-aligner) + - names: + - -m + - --analysis-mode + argument: arg (=seeking) + description: Specify which analysis workflow to use (seeking or streaming) + - names: + - -n + - --threads + argument: arg (=1) + description: Number of threads to use +version: ExpansionHunter v5.0.0 diff --git a/bio/yaml/bio.yaml b/bio/yaml/bio.yaml index 08f25b4f..1b5a5527 100644 --- a/bio/yaml/bio.yaml +++ b/bio/yaml/bio.yaml @@ -59,7 +59,7 @@ subcommands: description: fields - name: fetch description: download GenBank/ENSEMBL data - usage: bio download [-h] [-d ''] [-t ''] [-f ''] [-l None] [acc ...] + usage: bio download [-h] [-d ''] [-t ''] [-f ''] [-l 100] [-o ''] [acc ...] options: - names: - -h @@ -84,8 +84,13 @@ subcommands: - names: - -l - --limit - argument: None + argument: "100" description: limit results + - names: + - -o + - --out + argument: '''''' + description: output file (used as prefix in for FASTQ) - name: fasta description: convert to FASTA usage: bio fasta [-h] [-s 1] [-e ''] [-t ''] [-i ''] [-m ''] [-g ''] [-r ''] [-p] [-T] [-R] [-G] [-A ''] [-o ''] [-F 1] [fnames ...] @@ -697,7 +702,7 @@ subcommands: - --tab argument: "" description: tab delimited (default is csv) -version: '1.5.9' +version: '1.6.0' tldr: | > bio is a bioinformatics toy to play with. > More information: . diff --git a/bio/yaml/glnexus_cli.yaml b/bio/yaml/glnexus_cli.yaml new file mode 100644 index 00000000..446adbfc --- /dev/null +++ b/bio/yaml/glnexus_cli.yaml @@ -0,0 +1,55 @@ +name: glnexus_cli +description: Merge and joint-call input gVCF files, emitting multi-sample BCF on standard output +usage: glnexus_cli [options] /vcf/file/1 .. /vcf/file/N +options: + - names: + - --dir + - -d + argument: DIR + description: 'scratch directory path (mustn''t already exist; default: ./GLnexus.DB)' + - names: + - --config + - -c + argument: X + description: 'configuration preset name or .yml filename (default: gatk)' + - names: + - --bed + - -b + argument: FILE + description: 'three-column BED file with ranges to analyze (if neither --range nor --bed: use full length of all contigs)' + - names: + - --list + - -l + argument: "" + description: expect given files to contain lists of gVCF filenames, one per line + - names: + - --more-PL + - -P + argument: "" + description: include PL from reference bands and other cases omitted by default + - names: + - --squeeze + - -S + argument: "" + description: reduce pVCF size by suppressing detail in cells derived from reference bands + - names: + - --trim-uncalled-alleles + - -a + argument: "" + description: remove alleles with no output GT calls in postprocessing + - names: + - --mem-gbytes + - -m + argument: X + description: 'memory budget, in gbytes (default: most of system memory)' + - names: + - --threads + - -t + argument: X + description: 'thread budget (default: all hardware threads)' + - names: + - --help + - -h + argument: "" + description: print this help message +version: v1.4.1-0-g68e25e5 diff --git a/bio/yaml/lofreq.yaml b/bio/yaml/lofreq.yaml new file mode 100644 index 00000000..7719ed3d --- /dev/null +++ b/bio/yaml/lofreq.yaml @@ -0,0 +1,775 @@ +name: lofreq +description: Fast and sensitive inference of SNVs and indels +usage: lofreq [options] +options: [] +subcommands: + - name: call + description: Call variants + usage: lofreq call [options] in.bam + options: + - names: + - -f + - --ref + argument: FILE + description: Indexed reference fasta file (gzip supported) [null] + - names: + - -o + - --out + argument: FILE + description: Vcf output file [- = stdout] + - names: + - -r + - --region + argument: STR + description: Limit calls to this region (chrom:start-end) [null] + - names: + - -l + - --bed + argument: FILE + description: List of positions (chr pos) or regions (BED) [null] + - names: + - -q + - --min-bq + argument: INT + description: Skip any base with baseQ smaller than INT [6] + - names: + - -Q + - --min-alt-bq + argument: INT + description: Skip alternate bases with baseQ smaller than INT [6] + - names: + - -R + - --def-alt-bq + argument: INT + description: 'Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0]' + - names: + - -j + - --min-jq + argument: INT + description: Skip any base with joinedQ smaller than INT [0] + - names: + - -J + - --min-alt-jq + argument: INT + description: Skip alternate bases with joinedQ smaller than INT [0] + - names: + - -K + - --def-alt-jq + argument: INT + description: 'Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0]' + - names: + - -B + - --no-baq + argument: "" + description: Disable use of base-alignment quality (BAQ) + - names: + - -A + - --no-idaq + argument: "" + description: Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging) + - names: + - -D + - --del-baq + argument: "" + description: Delete pre-existing BAQ values, i.e. compute even if already present in BAM + - names: + - -e + - --no-ext-baq + argument: "" + description: Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag) + - names: + - -m + - --min-mq + argument: INT + description: Skip reads with mapping quality smaller than INT [0] + - names: + - -M + - --max-mq + argument: INT + description: Cap mapping quality at INT [255] + - names: + - -N + - --no-mq + argument: "" + description: Don't merge mapping quality in LoFreq's model + - names: + - --call-indels + argument: "" + description: 'Enable indel calls (note: preprocess your file to include indel alignment qualities!)' + - names: + - --only-indels + argument: "" + description: Only call indels; no SNVs + - names: + - -s + - --src-qual + argument: "" + description: Enable computation of source quality + - names: + - -S + - --ign-vcf + argument: FILE + description: Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas + - names: + - -T + - --def-nm-q + argument: INT + description: If >= 0, then replace non-match base qualities with this default value [-1] + - names: + - -a + - --sig + argument: "" + description: P-Value cutoff / significance level [0.010000] + - names: + - -b + - --bonf + argument: "" + description: Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic'] + - names: + - -C + - --min-cov + argument: INT + description: 'Test only positions having at least this coverage [1] (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)' + - names: + - -d + - --max-depth + argument: INT + description: Cap coverage at this depth [1000000] + - names: + - --illumina-1.3 + argument: "" + description: Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded + - names: + - --use-orphan + argument: "" + description: Count anomalous read pairs (i.e. where mate is not aligned properly) + - names: + - --plp-summary-only + argument: "" + description: No variant calling. Just output pileup summary per column + - names: + - --no-default-filter + argument: "" + description: Don't run default 'lofreq filter' automatically after calling variants + - names: + - --force-overwrite + argument: "" + description: Overwrite any existing output + - names: + - --verbose + argument: "" + description: Be verbose + - names: + - --debug + argument: "" + description: Enable debugging + - name: call-parallel + description: Call variants in parallel + usage: "" + options: [] + - name: somatic + description: Call somatic variants + usage: lofreq somatic [-h] [-v] -n NORMAL -t TUMOR -o OUTPREFIX -f REF [-l BED] [-d DBSNP] [--threads NUM_THREADS] [--tumor-mtc {bonf,holm-bonf,fdr}] [--tumor-mtc-alpha TUMOR_MTC_ALPHA] [--indel-tumor-mtc {bonf,holm-bonf,fdr}] [--indel-tumor-mtc-alpha INDEL_TUMOR_MTC_ALPHA] [--call-indels] [--min-cov MIN_COV] [--germline] [-S IGN_VCF] [--use-orphan] [--baq-off] [--call-rlx-extra-args CALL_RLX_EXTRA_ARGS] [--no-src-qual] [--debug] [--continue] + options: + - names: + - -h + - --help + argument: "" + description: show this help message and exit + - names: + - -v + - --verbose + argument: "" + description: Be verbose + - names: + - -n + - --normal + argument: NORMAL + description: Normal BAM file + - names: + - -t + - --tumor + argument: TUMOR + description: Tumor BAM file + - names: + - -o + - --outprefix + argument: OUTPREFIX + description: Prefix for output files + - names: + - -f + - --ref + argument: REF + description: Reference fasta file + - names: + - -l + - --bed + argument: BED + description: BED file listing regions to restrict analysis to + - names: + - -d + - --dbsnp + argument: DBSNP + description: vcf-file (bgzipped and index with tabix) containing known germline variants (e.g. dbsnp for human + - names: + - --threads + argument: NUM_THREADS + description: Use this many threads for each call + - names: + - --tumor-mtc + argument: '{bonf,holm-bonf,fdr}' + description: 'Type of multiple testing correction for tumor (default: bonf)' + - names: + - --tumor-mtc-alpha + argument: TUMOR_MTC_ALPHA + description: 'Multiple testing correction alpha for tumor (default: 1.000000)' + - names: + - --indel-tumor-mtc + argument: '{bonf,holm-bonf,fdr}' + description: 'Type of multiple testing correction for tumor (default: bonf)' + - names: + - --indel-tumor-mtc-alpha + argument: INDEL_TUMOR_MTC_ALPHA + description: 'Multiple testing correction alpha for tumor (default: 0.010000)' + - names: + - --call-indels + argument: "" + description: Also call indels (see documentation on how to preprocess your BAM files) + - names: + - --min-cov + argument: MIN_COV + description: 'Minimum coverage for somatic calls (default: 7)' + - names: + - --germline + argument: "" + description: Also list germline calls in separate file + - names: + - -S + - --ign-vcf + argument: IGN_VCF + description: Ignore variants in this vcf-file for source quality computation in tumor (collides with --no-src-qual). Default is to use (stringently filtered) predictions in normal sample + - names: + - --use-orphan + argument: "" + description: Use orphaned/anomalous reads from pairs in all samples + - names: + - --baq-off + argument: "" + description: Switch use of BAQ off in all samples + - names: + - --call-rlx-extra-args + argument: CALL_RLX_EXTRA_ARGS + description: Extra arguments to call_rlx (replace dashes with @) + - names: + - --no-src-qual + argument: "" + description: Disable use of source quality in tumor (see also -V) + - names: + - --debug + argument: "" + description: Enable debugging + - names: + - --continue + argument: "" + description: continue interrupted run. Will reuse existing files, assuming they are complete and created with identical options! + - name: viterbi + description: Viterbi realignment + usage: lofreq viterbi [options] in.bam + options: + - names: + - -f + - --ref + argument: FILE + description: Indexed reference fasta file [null] + - names: + - -k + - --keepflags + argument: "" + description: Don't delete flags MC, MD, NM and A, which are all prone to change during realignment. + - names: + - -q + - --defqual + argument: INT + description: Assume INT as quality for all bases with BQ2. Default (=-1) is to use median quality of bases in read. + - names: + - -o + - --out + argument: FILE + description: Output BAM file [- = stdout = default] + - names: + - --verbose + argument: "" + description: Be verbose + - name: indelqual + description: Insert indel qualities + usage: lofreq indelqual [options] in.bam + options: + - names: + - -u + - --uniform + argument: INT[,INT] + description: Add this indel quality uniformly to all bases. Use two comma separated values to specify insertion and deletion quality separately. (clashes with --dindel) + - names: + - --dindel + argument: "" + description: Add Dindel's indel qualities (Illumina specific) (clashes with -u; needs --ref) + - names: + - -f + - --ref + argument: "" + description: Reference sequence used for mapping (Only required for --dindel) + - names: + - -o + - --out + argument: FILE + description: Output BAM file [- = stdout = default] + - names: + - --verbose + argument: "" + description: Be verbose + - name: alnqual + description: Insert base and indel alignment qualities + usage: lofreq alnqual [options] + options: + - names: + - -b + argument: "" + description: BAM output (instead of SAM) + - names: + - -u + argument: "" + description: Uncompressed BAM output (for piping) + - names: + - -S + argument: "" + description: The input is SAM with header + - names: + - -e + argument: "" + description: Use default instead of extended BAQ (the latter gives better sensitivity but lower specificity) + - names: + - -B + argument: "" + description: Don't compute base alignment qualities + - names: + - -A + argument: "" + description: Don't compute indel alignment qualities + - names: + - -r + argument: "" + description: Recompute i.e. overwrite existing values + - name: checkref + description: Check that reference fasta and BAM file match + usage: lofreq checkref ref.fa in.bam + options: [] + - name: filter + description: Filter variants in VCF file + usage: lofreq filter [options] -i input.vcf -o output.vcf + options: + - names: + - -i + - --in + argument: FILE + description: VCF input file (no streaming supported; gzip supported) + - names: + - -o + - --out + argument: FILE + description: 'VCF output file (default: - for stdout; gzip supported).' + - names: + - -v + - --cov-min + argument: INT + description: Minimum coverage allowed (<1=off) + - names: + - -V + - --cov-max + argument: INT + description: Maximum coverage allowed (<1=off) + - names: + - -a + - --af-min + argument: FLOAT + description: Minimum allele freq allowed (<1=off) + - names: + - -A + - --af-max + argument: FLOAT + description: Maximum allele freq allowed (<1=off) + - names: + - -B + - --sb-thresh + argument: INT + description: Maximum phred-value allowed. Conflicts with -b. + - names: + - -b + - --sb-mtc + argument: STRING + description: Multiple testing correction type. One of 'bonf', 'holm' or 'fdr'. Conflicts with -B + - names: + - -c + - --sb-alpha + argument: FLOAT + description: Multiple testing correction pvalue threshold + - names: + - --sb-no-compound + argument: "" + description: Don't use compound filter + - names: + - --sb-incl-indels + argument: "" + description: Apply SB filter to indels as well + - names: + - -Q + - --snvqual-thresh + argument: INT + description: Minimum phred-value allowed. Conflicts with -q + - names: + - -q + - --snvqual-mtc + argument: STRING + description: Multiple testing correction type. One of 'bonf', 'holm' or 'fdr'. Conflicts with -Q + - names: + - -r + - --snvqual-alpha + argument: FLOAT + description: Multiple testing correction pvalue threshold + - names: + - -s + - --snvqual-ntests + argument: INT + description: Number of performed SNV tests for multiple testing correction + - names: + - -K + - --indelqual-thresh + argument: INT + description: Minimum phred-value allowed. Conflicts with -q + - names: + - -k + - --indelqual-mtc + argument: STRING + description: Multiple testing correction type. One of 'bonf', 'holm' or 'fdr'. Conflicts with -Q + - names: + - -l + - --indelqual-alpha + argument: FLOAT + description: Multiple testing correction pvalue threshold + - names: + - -m + - --indelqual-ntests + argument: INT + description: Number of performed indel tests for multiple testing correction + - names: + - --only-indels + argument: "" + description: Keep InDels only + - names: + - --only-snvs + argument: "" + description: Keep SNVs only + - names: + - --print-all + argument: "" + description: Print all, not just passed variants + - names: + - --no-defaults + argument: "" + description: Remove all default filter settings + - names: + - --verbose + argument: "" + description: Be verbose + - names: + - --debug + argument: "" + description: Enable debugging + - name: uniq + description: Test whether variants predicted in only one sample really are unique + usage: lofreq uniq [options] indexed-in.bam + options: + - names: + - -v + - --vcf-in + argument: FILE + description: Input vcf file listing variants [- = stdin; gzip supported] + - names: + - -o + - --vcf-out + argument: FILE + description: Output vcf file [- = stdout; gzip supported] + - names: + - -f + - --uni-freq + argument: "" + description: Assume variants have uniform test frequency of this value (unused if <=0) [-1.000000] + - names: + - -t + - --uniq-thresh + argument: INT + description: Minimum uniq phred-value required. Conflicts with -m. 0 for off (default=0) + - names: + - -m + - --uniq-mtc + argument: STRING + description: Uniq multiple testing correction type. One of 'bonf', 'holm' or 'fdr'. (default=MTC_FDR) + - names: + - -a + - --uniq-alpha + argument: FLOAT + description: Uniq Multiple testing correction p-value threshold (default=0.001000) + - names: + - -n + - --uniq-ntests + argument: INT + description: Uniq multiple testing correction p-value threshold (default=#vars) + - names: + - --output-all + argument: "" + description: Report all variants instead of only the ones, marked unique. Note, that variants already filtered in input will not be printed. + - names: + - --use-det-lim + argument: "" + description: Report variants if they are above implied detection limit Default is to use binomial test to check for frequency differences + - names: + - --use-orphan + argument: "" + description: Don't ignore anomalous read pairs / orphan reads + - names: + - --verbose + argument: "" + description: Be verbose + - names: + - --debug + argument: "" + description: Enable debugging + - name: plpsummary + description: Print pileup summary per position + usage: lofreq call [options] in.bam + options: + - names: + - -f + - --ref + argument: FILE + description: Indexed reference fasta file (gzip supported) [null] + - names: + - -o + - --out + argument: FILE + description: Vcf output file [- = stdout] + - names: + - -r + - --region + argument: STR + description: Limit calls to this region (chrom:start-end) [null] + - names: + - -l + - --bed + argument: FILE + description: List of positions (chr pos) or regions (BED) [null] + - names: + - -q + - --min-bq + argument: INT + description: Skip any base with baseQ smaller than INT [6] + - names: + - -Q + - --min-alt-bq + argument: INT + description: Skip alternate bases with baseQ smaller than INT [6] + - names: + - -R + - --def-alt-bq + argument: INT + description: 'Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0]' + - names: + - -j + - --min-jq + argument: INT + description: Skip any base with joinedQ smaller than INT [0] + - names: + - -J + - --min-alt-jq + argument: INT + description: Skip alternate bases with joinedQ smaller than INT [0] + - names: + - -K + - --def-alt-jq + argument: INT + description: 'Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0]' + - names: + - -B + - --no-baq + argument: "" + description: Disable use of base-alignment quality (BAQ) + - names: + - -A + - --no-idaq + argument: "" + description: Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging) + - names: + - -D + - --del-baq + argument: "" + description: Delete pre-existing BAQ values, i.e. compute even if already present in BAM + - names: + - -e + - --no-ext-baq + argument: "" + description: Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag) + - names: + - -m + - --min-mq + argument: INT + description: Skip reads with mapping quality smaller than INT [0] + - names: + - -M + - --max-mq + argument: INT + description: Cap mapping quality at INT [255] + - names: + - -N + - --no-mq + argument: "" + description: Don't merge mapping quality in LoFreq's model + - names: + - --call-indels + argument: "" + description: 'Enable indel calls (note: preprocess your file to include indel alignment qualities!)' + - names: + - --only-indels + argument: "" + description: Only call indels; no SNVs + - names: + - -s + - --src-qual + argument: "" + description: Enable computation of source quality + - names: + - -S + - --ign-vcf + argument: FILE + description: Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas + - names: + - -T + - --def-nm-q + argument: INT + description: If >= 0, then replace non-match base qualities with this default value [-1] + - names: + - -a + - --sig + argument: "" + description: P-Value cutoff / significance level [0.010000] + - names: + - -b + - --bonf + argument: "" + description: Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic'] + - names: + - -C + - --min-cov + argument: INT + description: 'Test only positions having at least this coverage [1] (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)' + - names: + - -d + - --max-depth + argument: INT + description: Cap coverage at this depth [1000000] + - names: + - --illumina-1.3 + argument: "" + description: Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded + - names: + - --use-orphan + argument: "" + description: Count anomalous read pairs (i.e. where mate is not aligned properly) + - names: + - --plp-summary-only + argument: "" + description: No variant calling. Just output pileup summary per column + - names: + - --no-default-filter + argument: "" + description: Don't run default 'lofreq filter' automatically after calling variants + - names: + - --force-overwrite + argument: "" + description: Overwrite any existing output + - names: + - --verbose + argument: "" + description: Be verbose + - names: + - --debug + argument: "" + description: Enable debugging + - name: vcfset + description: VCF set operations + usage: lofreq vcfset [options] -a op -1 1.vcf -2 2.vcf + options: + - names: + - "-1" + - --vcf1 + argument: FILE + description: 1st VCF input file (bgzip supported) + - names: + - "-2" + - --vcf2 + argument: FILE + description: 2nd VCF input file (mandatory - except for concat - and needs to be tabix indexed) + - names: + - -o + - --vcfout + argument: "" + description: 'VCF output file (default: - for stdout; gzip supported).' + - names: + - -a + - --action + argument: "" + description: 'Set operation to perform: intersect, complement or concat. - intersect = vcf1 AND vcf2. - complement = vcf1 \ vcf2. - concat = vcf1 + vcf2 ... vcfn (output as in file order, i.e. output not necessarily sorted!)' + - names: + - -I + - --add-info + argument: STR + description: Add info field, e.g. 'SOMATIC' + - names: + - --count-only + argument: "" + description: Don't print bases, just numbers + - names: + - --only-pos + argument: "" + description: Disable allele-awareness by using position only (ignoring bases) as key for storing and comparison + - names: + - --only-passed + argument: "" + description: Ignore variants marked as filtered + - names: + - --only-snvs + argument: "" + description: Ignore anything but SNVs in both input files + - names: + - --only-indels + argument: "" + description: Ignore anything but indels in both input files + - names: + - --verbose + argument: "" + description: Be verbose + - names: + - --debug + argument: "" + description: Enable debugging + - name: version + description: Print version info + usage: "" + options: [] + - name: idxstats + description: Print stats for indexed BAM file + usage: samtools idxstats + options: [] + - name: vcfplot + description: Plot VCF statistics + usage: "" + options: [] +version: 'version: 2.1.5' diff --git a/bio/zsh b/bio/zsh index 9b23c066..599d4d10 160000 --- a/bio/zsh +++ b/bio/zsh @@ -1 +1 @@ -Subproject commit 9b23c066dade960d4e5ea574357207ee093dd6e8 +Subproject commit 599d4d1075a6b2a6e31c1742cce00218c212e691