Description

Given baseline and comparison sets of variants, calculate the recall/precision/f-measure

Input

name:type
description
pattern

meta:map

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

vcf:file

Input SV VCF file

*.vcf.gz

tbi:file

Input SV VCF index file

*.vcf.gz.tbi

truth_vcf:file

Input VCF file with truth SVs

*.vcf.gz

truth_tbi:file

Input VCF index file with truth SVs

*.vcf.gz.tbi

bed:file

BED file containing regions to compare

*.bed

meta2:map

Groovy Map containing fasta information e.g. [ id:'test', single_end:false ]

fasta:file

Reference FASTA file

*.{fasta,fa,fna}

meta3:map

Groovy Map containing fasta index information e.g. [ id:'test', single_end:false ]

fai:file

Reference FASTA index file

*.fai

Output

name:type
description
pattern

fn_vcf

meta:map

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

*.fn.vcf.gz:file

VCF file with false negatives

*.fn.vcf.gz

fn_tbi

meta:map

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

*.fn.vcf.gz.tbi:file

VCF index file with false negatives

*.fn.vcf.gz.tbi

fp_vcf

meta:map

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

*.fp.vcf.gz:file

VCF file with false positives

*.fp.vcf.gz

fp_tbi

meta:map

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

*.fp.vcf.gz.tbi:file

VCF index file with false positives

*.fp.vcf.gz.tbi

tp_base_vcf

meta:map

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

*.tp-base.vcf.gz:file

VCF file with base true positives

*.tp-base.vcf.gz

tp_base_tbi

meta:map

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

*.tp-base.vcf.gz.tbi:file

VCF index file with base true positives

*.tp-base.vcf.gz.tbi

tp_comp_vcf

meta:map

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

*.tp-comp.vcf.gz:file

VCF file with compared true positives

*.tp-comp.vcf.gz

tp_comp_tbi

meta:map

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

*.tp-comp.vcf.gz.tbi:file

VCF index file with compared true positives

*.tp-comp.vcf.gz.tbi

summary

meta:map

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

*.summary.json:file

Summary JSON file with results from the benchmark

*.summary.json

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
variantbenchmarking
maintainer
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub