gnomad-browser icon indicating copy to clipboard operation
gnomad-browser copied to clipboard

Display AN for non-UKB exome subset

Open ch-kr opened this issue 7 months ago • 1 comments

A user wrote in asking about the allele numbers (AN) for this variant. I realized from their question that the non-UKB ANs are not being displayed when that dataset is selected: Full gnomAD v4.1 dataset: image Non-UKB subset of gnomAD v4.1: image

The AN of the full v4.1 exomes is 1458958, so >729k samples have defined ANs at this site. Checking our all sites AN downloadable HT confirms that this variant has a defined non-UKB AN:

ht = hl.read_table('gs://gcp-public-data--gnomad/release/4.1/ht/exomes/gnomad.exomes.v4.1.allele_number_all_sites.ht')
ht = hl.filter_intervals(ht, [hl.parse_locus_interval>>> ht = hl.filter_intervals(ht, [hl.parse_locus_interval('chr3:10052405-10052406', reference_genome='GRCh38')])
# 167 is `{'group': 'adj', 'subset': 'non_ukb'}` per `ht.strata_meta`
ht = ht.annotate(adj=ht.AN[0], non_ukb=ht.AN[167])
ht.show()
image

Would it be possible to update the browser to display the non-UKB ANs when they exist?

ch-kr avatar Jul 19 '24 20:07 ch-kr