Description

Deconstruct snarls present in a variation graph in GFA format to variants in VCF format

Input

name:type
description
pattern

meta:map

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

]

gfa:file

Variation graph in GFA format

*.{gfa}

pb:file

Optional snarls file (from vg snarls) to avoid recomputing. Usually ends with “pb”. See “vg snarls”.

*.{pb}

gbwt:file

Optional GBWT file (from vg gbwt) so to only consider alt traversals that correspond to GBWT threads FILE.

*.{gbwt}

Output

name:type
description
pattern

vcf

meta:map

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

]

*.vcf:file

Variants in VCF format

*.{vcf}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

vg
MIT

Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.

github.com/vgteam/vg github.com/vgteam/vg/wiki
maintainer
Github user heuermh, @subwaystation
get in touch
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