Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

gfa{:bash}

:file

Variation graph in GFA format

*.{gfa}

pb{:bash}

:file

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

*.{pb}

gbwt{:bash}

: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{:bash}

meta{:bash}

:map

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

*.vcf{:bash}

:file

Variants in VCF format

*.{vcf}

versions{:bash}

versions.yml{:bash}

: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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