Hi fantastic hail team, Here is my simple question: let’s say I have a list of genes("/path/gene_list.tsv") and I would like to extract the gnomad(v2/v3) data for this gene list. I have tried it by below code and I am not getting the results as expected. Could you please help with where I do it wr…

[image] amirfeizi: Also why when I try to download the hail table from gs:// it only can be downloaded as hail table not hail matrixtable The released gnomAD data is site-level summary data, not the genotype-level matrix table. The genotypes cannot be made public for privacy reasons. [ima…

Thanks a lot for the reply, very useful (clearly I need more practice to adapt hail expression!). However, I have tried it, and running the last line ht_filt = ht_pc.filter(genes_as_hail_literal.contains(ht_gene_symbol)) got this error: TypeError: 'SetExpression.contains' expects 'item' to be the…

ah, it’s a doubly-nested array! I think you can do: ht_pc.filter(hl.len(genes_as_hail_literal.intersection(hl.set(ht_gene_symbol))) > 0)

Hi tpoterba, I follow your solution about filtering gnomad data with a list of gene symbol. However, I don’t know why after filtering, I got the same number of records (variants). Could you please take a look at my code below. Many thanks! ht = hl.read_table(“path/gnomad.exomes.r2.1.sites.ht/”) …

Querying gnomad using hail table by gene symbol

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Querying gnomad using hail table by gene symbol

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