modules/bcftools_stats

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

VCF input file

The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.

Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)

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

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

Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed).
e.g. ‘exons.tsv.gz’

Faidx indexed reference sequence file to determine INDEL context.
e.g. ‘reference.fa’