Description

Split VCF by chunks or regions, creating multiple VCFs.

Input

name:type
description
pattern

meta:map

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

]

vcf:file

The input VCF to scatter

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

tbi:file

Optional index of the input VCF

*.tbi

sites_per_chunk:integer

How many variants should be in each output file Either this or scatter or scatter_file have to be given

scatter:string

A comma delimited list of regions to scatter into Either this or sites_per_chunk or scatter_file have to be given

scatter_file:file

A file containing a region on each line with an optional second column containing the filename Either this or sites_per_chunk or scatter have to be given

regions:file

Optional file containing the regions to work on

*.bed

targets:file

Optional file containing the regions to work on (but streams instead of index-jumping)

*.bed

Output

name:type
description
pattern

scatter

meta:map

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

]

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

The resulting files of the scattering

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

tbi

meta:map

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

]

*.tbi:file

Alternative VCF file index

*.tbi

csi

meta:map

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

]

*.csi:file

Default VCF file index

*.csi

versions

versions.yml:file

File containing software versions

versions.yml