Description

Extracts fields from VCF or BCF files and outputs them in user-defined format.

Input

name:type
description
pattern

meta:map

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

]

vcf:file

The vcf file to be qeuried.

*.{vcf.gz, vcf}

tbi:file

The tab index for the VCF file to be inspected.

*.tbi

regions:file

Optionally, restrict the operation to regions listed in this file.

targets:file

Optionally, restrict the operation to regions listed in this file (doesn’t rely upon index files)

samples:file

Optional, file of sample names to be included or excluded. e.g. ‘file.tsv’

Output

name:type
description
pattern

output

meta:map

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

]

*.${suffix}:file

BCFTools query output file

versions

versions.yml:file

File containing software versions

versions.yml

Tools

query
MIT

Extracts fields from VCF or BCF files and outputs them in user-defined format.