Gnomad MAF question
I know that alternative allele is not the same as a minor allele for many cases. I am looking for Minor Allele Frequency values (MAF) for gnomad data. How would I obtain that?
Looking at this page, I see Allele Frequency which is alternative allele frequency: https://gnomad.broadinstitute.org/variant/1-55051215-G-GA?dataset=gnomad_r4
Is there a way to convert Gnomad's allele frequency which is based on the alternative allele to minor allele frequency?
Thanks!
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Minor allele freq for a biallelic site is basically whichever number is lesser. You can simply use the logic
x > 0.5? 1-x : xto get the MAF. Might be more robust if you download the gnomad VCF and process it locally.