Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

Input SV VCF file

*.vcf.gz

tbi{:bash}

:file

Input SV VCF index file

*.vcf.gz.tbi

truth_vcf{:bash}

:file

Input VCF file with truth SVs

*.vcf.gz

truth_tbi{:bash}

:file

Input VCF index file with truth SVs

*.vcf.gz.tbi

bed{:bash}

:file

BED file containing regions to compare

*.bed

meta2{:bash}

:map

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

fasta{:bash}

:file

Reference FASTA file

*.{fasta,fa,fna}

meta3{:bash}

:map

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

fai{:bash}

:file

Reference FASTA index file

*.fai

Output

name:type
description
pattern

fn_vcf{:bash}

meta{:bash}

:map

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

*.fn.vcf.gz{:bash}

:file

VCF file with false negatives

*.fn.vcf.gz

fn_tbi{:bash}

meta{:bash}

:map

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

*.fn.vcf.gz.tbi{:bash}

:file

VCF index file with false negatives

*.fn.vcf.gz.tbi

fp_vcf{:bash}

meta{:bash}

:map

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

*.fp.vcf.gz{:bash}

:file

VCF file with false positives

*.fp.vcf.gz

fp_tbi{:bash}

meta{:bash}

:map

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

*.fp.vcf.gz.tbi{:bash}

:file

VCF index file with false positives

*.fp.vcf.gz.tbi

tp_base_vcf{:bash}

meta{:bash}

:map

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

*.tp-base.vcf.gz{:bash}

:file

VCF file with base true positives

*.tp-base.vcf.gz

tp_base_tbi{:bash}

meta{:bash}

:map

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

*.tp-base.vcf.gz.tbi{:bash}

:file

VCF index file with base true positives

*.tp-base.vcf.gz.tbi

tp_comp_vcf{:bash}

meta{:bash}

:map

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

*.tp-comp.vcf.gz{:bash}

:file

VCF file with compared true positives

*.tp-comp.vcf.gz

tp_comp_tbi{:bash}

meta{:bash}

:map

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

*.tp-comp.vcf.gz.tbi{:bash}

:file

VCF index file with compared true positives

*.tp-comp.vcf.gz.tbi

summary{:bash}

meta{:bash}

:map

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

*.summary.json{:bash}

:file

Summary JSON file with results from the benchmark

*.summary.json

log{:bash}

meta{:bash}

:map

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

*.log.txt{:bash}

:file

Log file from Truvari run

*.log.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
variantbenchmarking
maintainer
Github user nvnieuwk
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