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}

truth_vcf:file

A standard VCF to compare against

*.{vcf}

bed:file

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

*.bed

wittyer_config:file

Config file in json format used to specify per variant type settings. Used in place of include bed arguments. (optional)

*.json

Output

name:type
description
pattern

report

meta:map

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

*.json:file

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

*.json

bench_vcf

meta:map

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

*.vcf.gz:file

Updated query and truth entries merged into one file

*.vcf.gz

bench_vcf_tbi

meta:map

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

*.vcf.gz.tbi:file

Index of merged query and truth entries VCF file

*.vcf.gz.tbi

versions

versions.yml:file

File containing software versions

versions.yml

Tools

wittyer
BSD-2

Illumina tool for large variant benchmarking