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

meta (map)

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

]

version (file)

File containing software version

versions.yml

csi (file)

Default VCF file index file

*.csi

tbi (file)

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

*.tbi

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.