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_index (file)

The index of the called VCF (optional)

*.tbi

truth_vcf (file)

A standard VCF to compare against

*.{vcf,vcf.gz}

truth_vcf_index (file)

The index of the standard VCF (optional)

*.tbi

truth_bed (file)

A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)

*.bed

evaluation_bed (file)

A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)

*.bed

sdf (file)

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

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

tp_vcf (file)

A VCF file for the true positive variants

*.tp.vcf.gz

tp_tbi (file)

The index of the VCF file for the true positive variants

*.tp.vcf.gz.tbi

fn_vcf (file)

A VCF file for the false negative variants

*.fn.vcf.gz

fn_tbi (file)

The index of the VCF file for the false negative variants

*.fn.vcf.gz.tbi

fp_vcf (file)

A VCF file for the false positive variants

*.fp.vcf.gz

fp_tbi (file)

The index of the VCF file for the false positive variants

*.fp.vcf.gz.tbi

baseline_vcf (file)

A VCF file for the true positive variants from the baseline

*.tp-baseline.vcf.gz

baseline_tbi (file)

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

*.tp-baseline.vcf.gz.tbi

snp_roc (file)

TSV files containing ROC data for the SNPs

*.snp_roc.tsv.gz

non_snp_roc (file)

TSV files containing ROC data for all variants except SNPs

*.non_snp_roc.tsv.gz

weighted_roc (file)

TSV files containing weighted ROC data for all variants

*.weighted_snp_roc.tsv.gz

summary (file)

A TXT file containing the summary of the evaluation

*.summary.txt

phasing (file)

A TXT file containing the data on the phasing

*.phasing.txt
included in
raredisease variantbenchmarking
maintainer
Github user nvnieuwk
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Tools

rtgtools
BSD

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation

realtimegenomics.com/products/rtg-tools github.com/RealTimeGenomics/rtg-tools