How to calculate popmax values for gnomAD variants?
I'm trying to use the gnomAD data to build a noise filter. We want to filter variants from our .vcf's that have a popmax value greater than a certain threshold, but I'm having trouble figuring out how to calculate popmax.
We've already downloaded the gnomAD .vcf.bgz files (separated by chromosome). The tabix package was recommended to me as a way to easily handle and manipulate these large files. But I cannot figure out how to use tabix to accomplish this.
Does anyone know if it's possible to use tabix to infer popmax values for variants in a vcf?
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Did you figure out how? I am also new to this and have no idea how to proceed with the files
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