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broadinstitute / seqr

web-based analysis tool for rare disease genomics
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Display gnomad SV allele count (Hom= Het=) #2507

Open stephditroia opened 2 years ago

stephditroia commented 2 years ago

Is your feature request related to a problem? Please describe. Seqr displays gnomad SV allele frequency, but given the small SV dataset it is hard to interpret allele count.

Describe the solution you'd like We would like the gnomad SV hom and het number displayed similar to This Callset or the gnomad v2 and v3 hom count.

Additional context

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hanars commented 2 years ago

Unfortunately this is not data that was delivered to us. We would need to reach out to the Talkowski group to have them add this data to the callset, and then we would need to reload dat ato get this information. I think we would need @anneodonnell to help set priority on this

hanars commented 2 years ago

As requested in https://github.com/broadinstitute/seqr/issues/2593, we should also be showing AC once that is available

lynnpais commented 2 months ago

@bpblanken we need to look into this

lynnpais commented 2 months ago

@bpblanken HET counts are not showing for SNVs as well for gnomAD4. Do you need a separate ticket to track this?

Screenshot 2024-07-22 at 9 02 59 AM
bpblanken commented 2 months ago

@lynnpais

yeah, I think the snv_indel is a separate issue. Have we ever displayed Het for gnomadAD? Looks like we do have Hom count being passed through.

For SVs, I only see gnomAD_V2_AF, gnomAD_V2_AC, and gnomAD_V2_AN in the VCF, which is not sufficient to display Het. I'm looking into the WDL to see if this is something I can add during the SV annotation work I am doing.

lynnpais commented 2 months ago

We display SNV het counts for ExAC and TopMed, but for gnomAD v4 it is in the hover over. Would be good to be consistent. I think this is a separate browser things, not pipeline, so will submit a separate ticket for Hana.