Calculating minor allele frequency for GnomAD VCF file

Question

[Jamie Watson]

I have downloaded GnomAD vcf file and want to calculate the minor allele frequency of each variant in that file. But I am not quite sure how to do that. I have an INFO column which has AC,AF, AN in there. Does AF refers to minor allele frequency for that variant? If not then how can I calculate the minor allele frequency. I've given below three variants from the file just to show you what a gnomAD file looks like

chr1 905315 . C A 293.0 PASS AC=1;AN=143276;AF=6.97954e-06;variant_type=snv... chr1 905311 906011 chr1:905311-906011 63 . 905431 905432 0,0,0 2 70,528 0,172

chr1 905315 rs1489213119 C T 1432.0 PASS AC=1;AN=143276;AF=6.97954e-06;variant_type=snv... chr1 905311 906011 chr1:905311-906011 63 . 905431 905432 0,0,0 2 70,528 0,172

I am sorry if this is a basic question. I am new to bioinformatics and haven't been able to find a solution yet.

Answer 1

[Jeremy Leipzig]

Yes AF is the MAF here.

It bears mentioning that sometimes the variant might not necessarily be the less common allele in all populations, and the major allele might even confer something weakly deleterious. But in these two cases, they only saw one individual with this mutation.

Answer 2

[Kalin]

You can also directly get the AF from gnomAD. It is much faster and safer. I created a python package based on SQLite databases, where you can easily query all gnomAD variants for GRCh37/38. https://github.com/KalinNonchev/gnomAD_MAF I have precomputed SQLite databases for gnomAD WGS for GRCh37/38 in the description of the package. Please take a look there.

Best,