Extracts fields from VCF or BCF files and outputs them in user-defined format.
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
vcf:file
The vcf file to be queried.
*.{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
*.${suffix}:file
BCFTools query output file
versions
versions.yml:file
File containing software versions
versions.yml
