Description

Index VCF tools

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

VCF file (optionally GZIPPED)

*.{vcf,vcf.gz}

Output

name:type
description
pattern

csi{:bash}

meta{:bash}

:map

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

*.csi{:bash}

:file

Default VCF file index file

*.csi

tbi{:bash}

meta{:bash}

:map

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

*.tbi{:bash}

:file

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

*.tbi

versions_bcftools{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

bcftools{:bash}

:string

The tool name

bcftools --version | sed '1!d; s/^.*bcftools //'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

bcftools{:bash}

:string

The tool name

bcftools --version | sed '1!d; s/^.*bcftools //'{:bash}

:string

The command used to generate the version of the tool

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.

samtools.github.io/bcftools samtools.github.io/bcftools/howtos https://github.com/samtools/bcftools 10.1093/gigascience/giab008
included in
alleleexpressiongenomicrelatednessmagpacsomaticpacvarphaseimpute
maintainer
Github user jfy133
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