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SACGF / variantgrid

VariantGrid public repo
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Excluding somatic variants in gene search analysis #685

Open PeerArts opened 1 year ago

PeerArts commented 1 year ago

Hi guys,

I get regular requests from collaborators to look if we have seen germline variants in a specific gene within our AFHCS or GA cohorts. I've created a 'Gene Search' analysis to have a quick look in our dataset: https://variantgrid.com/analysis/2466/

I always run into the issue that the rare variants are called in a somatic dataset (like the genomics collaboration one), as artefacts in 1 or 2 of the reads.

Would it be possible to exclude certain (somatic) projects/.vcfs in a gene search analysis?

Thanks! Peer

davmlaw commented 1 year ago

Thanks Peer, yes I can see the need for that, and I think an exclude VCF filter would be the way to do it