Description

The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

query_vcf:file

A VCF with called variants to benchmark against the standard

*.{vcf,vcf.gz}

query_vcf_tbi:file

The index of the VCF file with called variants to benchmark against the standard

*.{vcf.gz.tbi, vcf.tbi}

truth_vcf:file

A standard VCF to compare against

*.{vcf,vcf.gz}

truth_vcf_tbi:file

The index of the standard VCF to compare against

*.{vcf.gz.tbi, vcf.tbi}

truth_bed:file

A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional) This input should be used to provide the golden truth BED files.

*.bed

regions_bed:file

A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional) This input should be used to provide the regions used by the analysis

*.bed

meta2:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

sdf:file

The SDF (RTG Sequence Data File) folder of the reference genome

Output

name:type
description
pattern

tp_vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.tp.vcf.gz:file

A VCF file for the true positive variants

*.tp.vcf.gz

tp_tbi

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.tp.vcf.gz.tbi:file

The index of the VCF file for the true positive variants

*.tp.vcf.gz.tbi

fn_vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.fn.vcf.gz:file

A VCF file for the false negative variants

*.fn.vcf.gz

fn_tbi

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.fn.vcf.gz.tbi:file

The index of the VCF file for the false negative variants

*.fn.vcf.gz.tbi

fp_vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.fp.vcf.gz:file

A VCF file for the false positive variants

*.fp.vcf.gz

fp_tbi

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.fp.vcf.gz.tbi:file

The index of the VCF file for the false positive variants

*.fp.vcf.gz.tbi

baseline_vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.tp-baseline.vcf.gz:file

A VCF file for the true positive variants from the baseline

*.tp-baseline.vcf.gz

baseline_tbi

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

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

The index of the VCF file for the true positive variants from the baseline

*.tp-baseline.vcf.gz.tbi

snp_roc

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.snp_roc.tsv.gz:file

TSV files containing ROC data for the SNPs

*.snp_roc.tsv.gz

non_snp_roc

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.non_snp_roc.tsv.gz:file

TSV files containing ROC data for all variants except SNPs

*.non_snp_roc.tsv.gz

weighted_roc

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.weighted_roc.tsv.gz:file

TSV files containing weighted ROC data for all variants

*.weighted_snp_roc.tsv.gz

summary

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.summary.txt:file

A TXT file containing the summary of the evaluation

*.summary.txt

phasing

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.phasing.txt:file

A TXT file containing the data on the phasing

*.phasing.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

rtgtools
BSD

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation

realtimegenomics.com/products/rtg-tools github.com/RealTimeGenomics/rtg-tools
included in
raredisease variantbenchmarking
maintainer
Github user nvnieuwk
get in touch
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