modules/aardvark_merge

A tool to evaluate and merge multiple variant calls into a consensus VCF.

variant callingvcfcomparisonconsensusmerging

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

Description

A tool to evaluate and merge multiple variant calls into a consensus VCF.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`vcfs`
`:file`

List of VCF files to be merged

*.{vcf.gz}

`indexes`
`:file`

List of index files for the input VCF files

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

`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 bed information

`bed`
`:file`

Optional BED file containing genomic regions to restrict the merge operation

*.{bed}

Output

name:type

description

pattern

`summary`

`meta`
`:map`

Groovy Map containing sample information

`*.summary.tsv`
`:file`

Global summary statistics of the variant merge

*.summary.tsv

`passing_vcf`

`meta`
`:map`

Groovy Map containing sample information

`*.passing.vcf.gz`
`:file`

Merged VCF file containing passing variants

*.passing.vcf.gz

`passing_vcf_index`

`meta`
`:map`

Groovy Map containing sample information

`*.passing.vcf.gz.tbi`
`:file`

Index file for the merged passing VCF

*.passing.vcf.gz.tbi

`passing_regions`

`meta`
`:map`

Groovy Map containing sample information

`*.regions.bed.gz`
`:file`

BED file of regions containing passing variants

*.regions.bed.gz

`passing_regions_index`

`meta`
`:map`

Groovy Map containing sample information

`*.regions.bed.gz.tbi`
`:file`

Index file for the passing regions BED

*.regions.bed.gz.tbi

`failed_regions`

`meta`
`:map`

Groovy Map containing sample information

`*.failed_regions.bed.gz`
`:file`

BED file of regions that failed merging criteria

*.failed_regions.bed.gz

`failed_regions_index`

`meta`
`:map`

Groovy Map containing sample information

`*.failed_regions.bed.gz.tbi`
`:file`

Index file for the failed regions BED

*.failed_regions.bed.gz.tbi

`runinfo`

`meta`
`:map`

Groovy Map containing sample information

`*.json`
`:file`

JSON file containing parameter settings used during the run

*.json

`versions_aardvark`

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

The name of the process

`aardvark`
`:string`

The name of the tool

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

The expression to obtain the version of the tool

Tools

aardvark
MIT

The aardvark merge command provides a method to merge variant calls. This functionality is helpful when multiple variant callers or technologies are used for the same sample. Merging variant sets can be complex and Aardvark simplifies this process by modeling the variants as haplotypes. This allows for different merge strategies for resolving conflicting variant sets.

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