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' ]

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' ]

fasta

:file

Reference FASTA file

*.{fasta,fa,fna}

meta3

:map

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

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' ]

*.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' ]

*.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' ]

*.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' ]

*.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' ]

*.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' ]

*.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' ]

*.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' ]

*.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' ]

*.summary.json

:file

Summary JSON file with results from the benchmark

*.summary.json

log

meta

:map

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

*.log.txt

:file

Log file from Truvari run

*.log.txt

versions_truvari

${task.process}

:string

The process the versions were collected from

truvari

:string

The name of the tool

truvari version | sed 's/Truvari v//'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

truvari

:string

The name of the tool

truvari version | sed 's/Truvari v//'

:eval

The expression to obtain the version of the tool

Tools

included in
variantbenchmarking
maintainer
Github user nvnieuwk
get in touch
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