I am trying to get the gnomad allele frequencies of variants in the VCF files (I share the screenshot of one example which allele frequency I want to have). I used the following protocols and operations:
I have two sets of AF values, I believe one retrieved from gnomad211_genome database, one retrieved from gnomad211_exome database. Here are the columns I get after the annotation: (2 of the each one with the same name: 2 AF, 2 AF_popmax, 2 AF_male... etc.)
AF AF_popmax AF_male AF_female AF_raw AF_afr AF_sas AF_amr AF_eas AF_nfe AF_fin AF_asj AF_oth non_topmed_AF_popmax non_neuro_AF_popmax non_cancer_AF_popmax controls_AF_popmax
But any of these columns have the value that I want (which can be seen in the screenshot I share) How can I get gnomad allele frequencies of the variants?
Also, another weird thing is that some variants have an AF values that are too much low, when I check them on gnomad database, they don't exist. How can I get some frequency values if the variants are not in the gnomad database, should I trust these too low values?
Thank you all!
Notice that the allele frequency is 0.2391