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Revision as of 12:23, 10 December 2014
, 12:23, 10 December 2014→Overview of GotCloud/GenomeSTRiP pipeline
In addition, if one wants to genotype structural variants from other structural variant caller, there is a step available.
In addition, if one wants to genotype structural variants from other structural variant caller, there is a step available.
* Third-party Genotyping and Filtering step : Perform genotyping on the variant sites specified by an input VCF, and also perform variant filtering.
* Third-party Genotyping and Filtering step : Perform genotyping on the variant sites specified by an input VCF, and also perform variant filtering.
== Command Line Usage of GenomeSTRiP pipeline ==
To see how to use GenomeSTRiP pipeline, type
perl $GC/bin/genomestrip.pl
ERROR: One of command options among --run-metadata, --run-discovery, --run-genotype, --run-thirdparty must be specified
ERROR: Missing required option, outdir
Usage:
/net/seqshop-server/home/mktrost/seqshop/gotcloud/bin/genomestrip.pl
[options]
Help Options:
-help Print out brief help message [OFF]
-man Print the full documentation in man page style [OFF]
Command options:
-run-metadata Create metadata [OFF]
-run-discovery Run variant discovery and filtering. Can run with --run-metadata together [OFF]
-run-genotype Run genotyping - requires to finish run-metadata and run-discovery [OFF]
-run-thirdparty Run genotyping and filtering of third-party sites [OFF]
Options for input/output data:
-gotcloudroot|gcroot STRGotCloud Root Directory []
-conf STR GotCloud configuration files []
-outdir STR Override's conf file's OUT_DIR. Used as the genomestrip output directory unless --out or GENOMESTRIP_OUT is set []
-list STR BAM list file containing ID and BAM path []
-out STR Output directory which stores subdirectories such as metadata/, discovery/, genotypes/, thirdparty/ unless overriden individually []
-metadata STR Output directory to store --run-metadata results. Default is [OUT]/metadata/ []
-discovery STR Output directory to store --run-discovery results. Default is [OUT]/discovery/ []
-genotype STR Output directory to store --run-genotype results. Default is [OUT]/genotype/ []
-thirdparty STR Output directory to store --run-thirdparty results. Default is [OUT]/thirdparty/ []
Advanced Options:
-tmp-dir STR temporary directory to store temporary files. Default is [OUT]/tmp []
-gs-dir STR GenomeSTRiP svtoolkit directory []
-param STR GenomeSTRIP parameter file []
-ref STR Reference FASTA file []
-mask STR Reference mask FASTA file []
-ploidy-map STR Ploidy map file []
-mosix-opt STR MOSIX options []
-region STR Region to focus on the variants []
-unit INT Number of variants to be genotyped per parallel run [100]
Additional Inputs:
-in-vcf STR Input site VCF files used for --run-genotype or --run-thirdparty. For --run-thirdparty, this argument is required. For --run-genotype, default is [OUT]/discovery/discovery.vcf []
-pass-only Genotype only PASS-filtered variants, default is OFF [OFF]
-skip-rc Skip precomputing read count [OFF]
-base-prefix STR Prefix of all files []
-bam-prefix STR Prefix of BAM files []
-ref-prefix STR Prefix of Reference FASTA files []
-no-phonehome Skip phone home functionality [OFF]
-make-base-name STR Specifies the basename for the makefile []
-verbose Specifies that additional details are to be printed out [OFF]
-dry-run Perform a dry-run that only produces Makefile but not run it [OFF]
-numjobs INT Number of jobs to concurrently run [1]
-autosomes Perform analysis only on autosomes [OFF]
== Running GotCloud/GenomeSTRiP Metadata Pipeline ==
== Running GotCloud/GenomeSTRiP Metadata Pipeline ==
