search

phenopolis / phenopolis_genomics_browser

Python API and React frontend for the Phenopolis Genomics Browser
https://dev-live.phenopolis.org
MIT License
31 stars 2 forks source link

Gnomad inconsistencies #337

Open alanwilter opened 3 years ago

alanwilter commented 3 years ago

For example, variant 14-76135756-T-C, which is found at https://gnomad.broadinstitute.org/variant/14-76135756-T-C?dataset=gnomad_r2_1, is missing in table gnomad.annotation_v3.

Querying for this chrom and position:

select * from gnomad.annotation_v3 av where av.chrom = '14' and av.pos = 76135756;
chrom   pos         ref alt ac      af
14      76,135,756  G   A   1,708   0.0119237

but this variant 14-76135756-G-A is not in gnomad (https://gnomad.broadinstitute.org/variant/14-76135756-G-A?dataset=gnomad_r2_1).

All above is related to GRCh37.

However, if I search both variants above in GRCh38, the reversed is presented, where 14-76135756-G-A is now found but not 14-76135756-T-C.

Looking at scripts/import_gnomad.py I just wonder how this script was run and where are the logs. Could be that we imported GRCh38 data rather than GRCh37?

I suggest having a look here https://gnomad.broadinstitute.org/downloads as well.

pontikos commented 3 years ago

I believe this is a strand issue ? @priesgo thoughts?