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’ ]

bam (file)

BAM/CRAM file

*.{bam,cram}

bai (file)

BAM index file. This is automatically found base on BAM input file name

*.{bai}

ref (file)

Reference fasta file

*.{fa, fasta, fas}

ref_fai (file)

Reference index file. This is automatically found based on referece input file name.

*.{.fai}

region_file (file)

File with a list of chromosome/locations in reference genome to genotype. One region per line in the format :-. This or --region (in ext.args) must be specified.

*

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)

VCF file with genotyped variants

*.{vcf.gz}

tbi (file)

VCF index file

*.{vcf.gz.tbi}
included in
pathogensurveillance
maintainer
Github user zachary-foster
get in touch
Ask a question on Slack Open an issue on GitHub

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