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| 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 == |