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