A large variant benchmarking tool analogous to hap.py for small variants.
meta
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
query_vcf
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
versions
File containing software versions
versions.yml
report
Detailed per-sample-pair, per-svtype, per-bin stats
bench_vcf
Updated query and truth entries merged into one file
*.vcf.gz
bench_vcf_tbi
Index of merged query and truth entries VCF file
*.vcf.gz.tbi
Illumina tool for large variant benchmarking
