Description

Index VCF tools

Input

name:type
description
pattern

meta:map

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

]

vcf:file

VCF file (optionally GZIPPED)

*.{vcf,vcf.gz}

Output

name:type
description
pattern

csi

meta:map

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

]

*.csi:file

Default VCF file index file

*.csi

tbi

meta:map

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

]

*.tbi:file

Alternative VCF file index file for larger files (activated with -t parameter)

*.tbi

versions

versions.yml:file

File containing software version

versions.yml

Tools

bcftools
MIT GPL-3.0-or-later

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.