Description

Sorts vcf files

Input

Name (Type)
Description
Pattern

meta (map)

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

]

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

vcf (file)

Sorted VCF file

*.{vcf}
included in
raredisease
author
Github user ramprasadn
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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