Generates stats from VCF files
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf
:file
VCF input file
*.{vcf}
tbi
The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.
*.tbi
meta2
regions
Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)
meta3
targets
Optionally, restrict the operation to regions listed in this file (doesn’t rely upon tbi index files)
meta4
samples
Optional, file of sample names to be included or excluded. e.g. ‘file.tsv’
meta5
exons
Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). e.g. ‘exons.tsv.gz’
meta6
fasta
Faidx indexed reference sequence file to determine INDEL context. e.g. ‘reference.fa’
stats
*stats.txt
Text output file containing stats
*_{stats.txt}
versions
versions.yml
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.
