Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

The VCF file to split

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

tbi (file)

OPTIONAL - The index of the input VCF/BCF

*.tbi

samples (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 (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 (file)

A BED file containing regions to use

*.bed

targets (file)

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

*.bed

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)

The resulting VCF files from the split

*.{vcf,vcf.gz,bcf,bcf.gz}
included in
phaseimpute
maintainer
Github user nvnieuwk
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