ExAC data with
hg38 coordinates has been around for filter-based annotation since late 2015, but it seems there is a systematic problem with the use of ExAC and 1000G lifted-over data data for annotation! Mainstream annotation softwares (Annovar, VEP and snpEff) fail to incorporate MAF for variants that their corresponding contig is reversed in the hg38 assembly. As a result, common variants in ExAC and 1000G populations might be misinterpreted as novel variant solely because annotation softwares fail to report corresponding MAF.
I was wondering if anyone here has come across the same problem and if so, how they have tackled this problem?