Description

Split VCF by sample, creating single- or multi-sample VCFs.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

The VCF file to split

*.{vcf,vcf.gz,bcf,bcf.gz}

tbi{:bash}

:file

OPTIONAL - The index of the input VCF/BCF

*.tbi

samples{:bash}

:file

A tab-separated file determining which samples should be in which output file column 1: The sample name(s) in the input file column 2: The sample name(s) to use in the output file (use - to keep the original name) column 3: The name of the output file Either this or a groups file should be given

*

groups{:bash}

:file

A tab-separated file determining which samples should be in which output file(s) column 1: The sample name(s) in the input file column 2: The sample name(s) to use in the output file (use - to keep the original name) column 3: The name of the output file(s) Either this or a samples file should be given

*

regions{:bash}

:file

A BED file containing regions to use

*.bed

targets{:bash}

:file

A BED file containing regions to use (but streams rather than index-jumps)

*.bed

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.{vcf,vcf.gz,bcf,bcf.gz}{:bash}

:file

The resulting VCF files from the split

*.{vcf,vcf.gz,bcf,bcf.gz}

tbi{:bash}

meta{:bash}

:map

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

*.tbi{:bash}

:file

TBI file

*.tbi

csi{:bash}

meta{:bash}

:map

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

*.csi{:bash}

:file

CSI file

*.csi

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
phaseimpute
maintainer
Github user nvnieuwk
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