broadinstitute / gnomad-browser

Explore gnomAD datasets on the web
https://gnomad.broadinstitute.org
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Variant display pages claims to just be showing Exome data but is showing Exome plus Genome data #1591

Open congenica-peter-fox opened 1 week ago

congenica-peter-fox commented 1 week ago

What you did:

I looked at the GnomAD 4.1 data for variant chr2:79195912-G-T

https://gnomad.broadinstitute.org/variant/2-79195912-G-T?dataset=gnomad_r4

What happened:

The foot of the Genetic Ancestry Group Frequencies table indicate that just exome data was being viewed

Screenshot 2024-06-28 at 15 00 02

However the total allele count from the Genetic Ancestry Group Frequencies table matches the allele count for the Exomes PLUS Genomes. Comparing the AN values with running a test sample through hail and the published GnomAD 4.1 data the allele counts do match the counts for just exomes.

congenica-peter-fox commented 1 week ago

Another page showing this behaviour is

https://gnomad.broadinstitute.org/variant/2-79195912-G-A?dataset=gnomad_r4