Description

Tools for population-scale genotyping using pangenome graphs.

Input

name:type
description
pattern

meta:map

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

vcf:file

VCF files

*.{vcf,vcf.gz}

Output

name:type
description
pattern

vcf

meta:map

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

*.vcf.gz:file

Concatenated VCF file

*.{vcf.gz}

tbi

meta:map

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

*.tbi:file

Concatenated VCF file index

*.{tbi}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

graphtyper
MIT

A graph-based variant caller capable of genotyping population-scale short read data sets while incoperating previously discovered variants.