I’m trying to decide which of the filtering allele frequency (FAF) fields from the vcf to use for filtering possible disease-associated mutants. I think I should use either fafmax_faf95_max or fafmax_faf95_max_joint (rather than faf95) but it’s not clear which “joint subset” the latter refers to. And subset of which larger set? Could this please be documented or clarified?
@pgarg ‘joint’ is exomes and genomes combined, not a subset, though the data might come from either one dataset or both. You may find an example on any variant page, and it’s explained in our gnomAD v4.0 blog post:
Updated filtering allele frequency
We have released a new, combined filtering allele frequency (FAF), which integrates variant frequencies across the 734,947 exomes and 76,215 genomes. The exome FAF and genome FAF are still listed on the variant pages as well.
If you have doubt which one to use, you may find this discussion helpful: Difference between popmax in the VCF and popmax/GrpmaxFAF in the website