Description

Sorts vcf files

Input

name:type
description
pattern

meta

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

vcf

:file

VCF file

*.{vcf,vcf.gz}

meta2

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fasta

:file

Reference genome fasta file

*.{fasta,fa}

meta3

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

dict

:file

Reference genome dictionary file

*.{dict}

Output

name:type
description
pattern

vcf

meta

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_sorted.vcf.gz

:file

Sorted VCF file

*.{vcf}

versions_picard

${task.process}

:string

The process the versions were collected from

picard

:string

The tool name

picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

picard

:string

The tool name

picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'

:string

The command used to generate the version of the tool

Tools

picard
MIT

Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format

broadinstitute.github.io/picard broadinstitute.github.io/picard/command-line-overview.html#SortVcf
included in
raredisease
maintainer
Github user ramprasadn
get in touch
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