An update: I just did a quick filtering on gnomAD-v4 versus v4.1 files, and the number of filtered variants were different (182467865 vs 181594644) so there is no issue with the AF in the new gnomAD files. The filtered variants in my cohort are not affected by the AF change in v4.1 and that might be because I only used non-ukb AF to filter variants. My question is resolved now. Thank you!
Hello,
Thank you for your response and the code. There might have been a misunderstanding. The variant counts comparison Iām doing is between the two versions of gnomAD. I was expecting that the variant counts change after using the v4.1 because of the issue with AF in v4; However for all the cases in our cohort the variant counts remained the same, which made me wonder if the AF in the new gnomAD release (v4.1) has been really corrected. See the following two lines as an example:
Case1 ā Filter (gnomAD v4 AF_non-ukb <= 0.01) = 524
Case1 ā Filter (gnomAD v4.1 AF_non-ukb <= 0.01) = 524