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

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

meta (map)

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

versions (file)

File containing software versions

versions.yml

fn_vcf (file)

VCF file with false negatives

*.fn.vcf.gz

fn_tbi (file)

VCF index file with false negatives

*.fn.vcf.gz.tbi

fp_vcf (file)

VCF file with false positives

*.fp.vcf.gz

fp_tbi (file)

VCF index file with false positives

*.fp.vcf.gz.tbi

tp_base_vcf (file)

VCF file with base true positives

*.tp-base.vcf.gz

tp_base_tbi (file)

VCF index file with base true positives

*.tp-base.vcf.gz.tbi

tp_comp_vcf (file)

VCF file with compared true positives

*.tp-comp.vcf.gz

tp_comp_tbi (file)

VCF index file with compared true positives

*.tp-comp.vcf.gz.tbi

summary (file)

Summary JSON file with results from the benchmark

*.summary.json