Generates stats from VCF files
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.
Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed).
Faidx indexed reference sequence file to determine INDEL context.
Text output file containing stats
File containing software versions
Parses VCF or BCF and produces text file stats which is suitable for
machine processing and can be plotted using plot-vcfstats.