Description

A large variant benchmarking tool analogous to hap.py for small variants.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

query_vcf (file)

A VCF with called variants to benchmark against the standard

*.{vcf,vcf.gz}

query_vcf_index (file)

The index of the called VCF (optional)

*.tbi

truth_vcf (file)

A standard VCF to compare against

*.{vcf,vcf.gz}

truth_vcf_index (file)

The index of the standard VCF (optional)

*.tbi

bed (file)

A BED file specifying regions to be included in the analysis (optional)

*.bed

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

versions (file)

File containing software versions

versions.yml

report (file)

Detailed per-sample-pair, per-svtype, per-bin stats

*.json

bench_vcf (file)

Updated query and truth entries merged into one file

*.vcf.gz

bench_vcf_tbi (file)

Index of merged query and truth entries VCF file

*.vcf.gz.tbi

Tools

wittyer
BSD-2

Illumina tool for large variant benchmarking