Extracts fields from VCF or BCF files and outputs them in user-defined format.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
The vcf file to be queried.
*.{vcf.gz, vcf}
tbi{:bash}
The tab index for the VCF file to be inspected.
*.tbi
regions{:bash}
Optionally, restrict the operation to regions listed in this file.
targets{:bash}
Optionally, restrict the operation to regions listed in this file (doesn’t rely upon index files)
samples{:bash}
Optional, file of sample names to be included or excluded. e.g. ‘file.tsv’
output{:bash}
*.${suffix}{:bash}
BCFTools query output file
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
