Variant qc AF field index meaning

#1

Hi

I was looking over the GWAS tutorial and was wondering what the [1] index means in

mt = mt.filter_rows(mt.variant_qc.AF[1] > 0.01)

Thanks

#2

The AF produced by variant_qc is an array with “one element per allele, including the reference”. AF[1] selects the allele frequency corresponding to the first alternate allele (AF[0] would be the reference). The dataset used in the tutorial is comprised of only biallelic variants, so we know this is the only alternate allele.