Variant filtering in seqr

[anjalijain22]

Hello,

Hope you're doing well! I am playing around with the variant search functionality in the new hail backend and noticed that the GQ filter (under call quality) doesn't remove variants that have a missing GQ value. I am wondering if this is by design or am I using the filter wrong? If I wanted to remove all variants that have a missing GQ, how would I go about doing that?

Screenshot of the call quality filters I used:

Screenshot of a variant returned in search results having a '-' for GQ:

Many thanks,
Anjali

[hanars]

The approved seqr joint calling pipelines should always be annotating GQ so I am not sure why you have raw data with no GQ in the first place. I would recommend making sure the data you injest is properly annotated with scores if you want to filter on them