Generates stats from VCF files
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
VCF input file
*.{vcf}
tbi{:bash}
The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.
*.tbi
meta2{:bash}
regions{:bash}
Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)
meta3{:bash}
targets{:bash}
Optionally, restrict the operation to regions listed in this file (doesn’t rely upon tbi index files)
meta4{:bash}
samples{:bash}
Optional, file of sample names to be included or excluded. e.g. ‘file.tsv’
meta5{:bash}
exons{:bash}
Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). e.g. ‘exons.tsv.gz’
meta6{:bash}
fasta{:bash}
Faidx indexed reference sequence file to determine INDEL context. e.g. ‘reference.fa’
stats{:bash}
*stats.txt{:bash}
Text output file containing stats
*_{stats.txt}
versions_bcftools{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
bcftools{:bash}
The tool name
bcftools --version | sed '1!d; s/^.*bcftools //'{:bash}
The command used to generate the version of the tool
versions{:bash}
Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats.
