From the discussions in previous questions, I understand that REF and ALT need not necessarily correspond to major and minor alleles. REF is from the ref genome and could very well be the minor allele for the variant.
I'd like to find out if a REF allele is a minor allele for any variant in my region of interest. One of the ways I could do this is to find out COUNT(variants) where af > 0.5 in my region of interest.
Would I be correct in assuming this approach will definitely give me the right answer? Is there any underlying assumption I'm missing before I use this as my standard approach?
Any anomalies you might have noted in your experience would help me. Thank you!