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

meta (map)

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

]

output (file)

BCFTools query output file

versions (file)

File containing software versions

versions.yml
included in
viralrecon
authors
Github user abhi18av Github user drpatelh
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

query
MIT

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

http://samtools.github.io/bcftools/bcftools.html http://www.htslib.org/doc/bcftools.html 10.1093/bioinformatics/btp352