search

KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
113 stars 27 forks source link

can't read vcf Strelka2 formated #120

Closed lmanchon closed 2 years ago

lmanchon commented 2 years ago

--Hi,

open-cravat failed when vcf input file is generated with Strelka2. Why ? see input vcf file in attachement somatic.snvs.vcf.zip

kmoad commented 2 years ago

Hi Imanchon. Thanks for the report. Especially thanks for attaching the vcf that caused the issue.

It looks like vcfs from Strelka2 don't have the GT field that oc uses to call whether or not a sample has the variant. This surprised me, as most other variant callers use it. I'm doing some reading to understand how Strelka formats their vcfs. Mostly this issue,

https://github.com/Illumina/strelka/issues/16

If you know anything more about how to parse Strelka vcfs, I'd be happy to hear it.

kmoad commented 2 years ago

Just put out vcf-converter 2.1.5 with a fix.

Variants in VCFs without the GT field will be annotated, but zygosity for all samples will be blank.

It's available for download, and up at run.opencravat.org.

Here's the commit: https://github.com/KarchinLab/open-cravat-modules-karchinlab/commit/127ae76eadc686d376f49743f73b0edb81e6d3c5