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

meta (map)

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

versions (file)

File containing software versions

versions.yml

vcf (file)

Concatenated VCF file

*.{vcf.gz}

tbi (file)

Concatenated VCF file index

*.{tbi}
included in
pathogensurveillance
author
Github user zachary-foster
get in touch
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Tools

graphtyper
MIT

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

github.com/DecodeGenetics/graphtyper github.com/DecodeGenetics/graphtyper/wiki/User-guide https://github.com/DecodeGenetics/graphtyper 10.1038/ng.3964