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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

scatter (file)

The resulting files of the scattering

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

csi (file)

Default VCF file index

*.csi

tbi (file)

Alternative VCF file index

*.tbi
maintainer
Github user nvnieuwk
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