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:false ]
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:false ]
*{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:false ]
*.tbi:file
Alternative VCF file index
*.tbi
csi
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.csi:file
Default VCF file index
*.csi
versions
versions.yml:file
File containing software versions
versions.yml
Tools
pluginscatter
MIT
Split VCF by chunks or regions, creating multiple VCFs.
