A large variant benchmarking tool analogous to hap.py for small variants.
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
query_vcf
:file
A VCF with called variants to benchmark against the standard
*.{vcf}
truth_vcf
A standard VCF to compare against
bed
A BED file specifying regions to be included in the analysis (optional)
*.bed
wittyer_config
Config file in json format used to specify per variant type settings. Used in place of include bed arguments. (optional)
*.json
report
Detailed per-sample-pair, per-svtype, per-bin stats
bench_vcf
*.vcf.gz
Updated query and truth entries merged into one file
bench_vcf_tbi
*.vcf.gz.tbi
Index of merged query and truth entries VCF file
versions_wittyer
${task.process}
:string
The process the versions were collected from
wittyer
The name of the tool
dotnet /opt/Wittyer/Wittyer.dll --version | sed '1!d ; s/witty.er //'
:eval
The expression to obtain the version of the tool
versions
Illumina tool for large variant benchmarking
