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:file
The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.
*.tbi
meta2:map
regions:file
Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)
meta3:map
targets:file
Optionally, restrict the operation to regions listed in this file (doesn’t rely upon tbi index files)
meta4:map
samples:file
Optional, file of sample names to be included or excluded. e.g. ‘file.tsv’
meta5:map
exons:file
Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). e.g. ‘exons.tsv.gz’
meta6:map
fasta:file
Faidx indexed reference sequence file to determine INDEL context. e.g. ‘reference.fa’
stats
*stats.txt:file
Text output file containing stats
*_{stats.txt}
versions
versions.yml:file
File containing software versions
versions.yml
Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats.
