populationgenomics / talos

Rare Disease variant reanalysis tool

MIT License

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Trust SV qualities #450

Closed MattWellie closed 1 week ago

MattWellie commented 1 week ago

Fixes

We're missing some CNV calls due to whole sites being failed due to a failing Q score at any one component participant

Proposed Changes

Scrap the Q score filter when processing SVs
... that's it
CyVCF2 doesn't have a way to check out the Q scores on the VCFs coming out of SVAnnotate via Hail, so it's non-trivial to flag some of these Q failures later.

cassimons commented 1 week ago

Can/should/do we just do variant-level GQ filtering on SVs? (default > 20) ?

MattWellie commented 1 week ago

Can/should/do we just do variant-level GQ filtering on SVs? (default > 20) ?

yes, I think so :D I'll do some poking to see if the site QUAL is intelligent, or taken from the first VCF in the merge. I'll get this in for now so we can see whether a completely unfiltered approach is viable