modules/aardvark_compare

A tool to evaluate variant calling performance by comparing a query VCF against a truth VCF.

variant callingbenchmarkingvcfcomparisonconsensus

https://github.com/nf-core/modules/[...]/modules/nf-core/aardvark/compare

Description

A tool to evaluate variant calling performance by comparing a query VCF against a truth VCF.

Input

name:type

description

pattern

`meta`
`:map`

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

`query_vcf`
`:file`

Query VCF file to be benchmarked

*.{vcf,vcf.gz}

`query_vcf_tbi`
`:file`

Index for the query VCF file

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

`truth_vcf`
`:file`

Truth VCF file containing the ground truth baseline

*.{vcf,vcf.gz}

`truth_vcf_tbi`
`:file`

Index for the truth VCF file

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

`regions_bed`
`:file`

Regions BED file containing genomic regions to restrict the evaluation

*.{bed}

`meta2`
`:map`

Groovy Map containing reference fasta information

`fasta`
`:file`

Reference genome fasta file

*.{fasta,fa,fasta.gz,fa.gz}

`meta3`
`:map`

Groovy Map containing stratification TSV information

`stratification_tsv`
`:file`

Optional TSV file defining stratification regions for fine grained benchmarking

*.tsv

`meta4`
`:map`

Groovy Map containing stratification BEDs information

`stratification_beds`
`:file`

Optional BED files corresponding to the regions defined in the stratification TSV

*.bed

Output

name:type

description

pattern

`summary`

`meta`
`:map`

Groovy Map containing sample information

`*.summary.tsv`
`:file`

Global summary statistics of the variant comparison

*.summary.tsv

`labelled_truth`

`meta`
`:map`

Groovy Map containing sample information

`*.truth.vcf.gz`
`:file`

Truth VCF file annotated with evaluation results

*.truth.vcf.gz

`labelled_query`

`meta`
`:map`

Groovy Map containing sample information

`*.query.vcf.gz`
`:file`

Query VCF file annotated with evaluation results

*.query.vcf.gz

`runinfo`

`meta`
`:map`

Groovy Map containing sample information

`*.json`
`:file`

JSON file containing parameter settings used during the run

*.json

`region_sequences`

`meta`
`:map`

Groovy Map containing sample information

`*.region_sequences.tsv.gz`
`:file`

Sequence level output for specific evaluated regions

*.region_sequences.tsv.gz

`region_summary`

`meta`
`:map`

Groovy Map containing sample information

`*.region_summary.tsv.gz`
`:file`

Summary statistics broken down by individual genomic regions

*.region_summary.tsv.gz

`versions_aardvark`

`${task.process}`
`:string`

The name of the process

`aardvark`
`:string`

The name of the tool

`aardvark compare --version 2>&1 | sed 's/aardvark-bio-compare //; s/-conda//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`aardvark`
`:string`

The name of the tool

`aardvark compare --version 2>&1 | sed 's/aardvark-bio-compare //; s/-conda//'`
`:eval`

The expression to obtain the version of the tool

Tools

aardvark
MIT

A benchmarking tool that constructs haplotype sequences and it enables basepair-level comparisons that work across all variant types. The program evaluates genotypes using traditional, strict exact-match scoring, while also allowing for implicit partial credit when variant calls are an inexact but close match.

github.com/PacificBiosciences/aardvark github.com/PacificBiosciences/aardvark/blob/main/docs/methods.md#compare-command https://github.com/PacificBiosciences/aardvark 10.1101/2025.10.03.680257