Could you please note in the documentation that the the ref/alt alleles need to be harmonized across studies? If the input VCF files are not harmonized, apparently APEX will not recognize the variant as shared across studies and therefore won't include the variant in the meta-analysis. Alternatively, a fix so APEX recognizes flipped ref/alt and alt/ref alleles as the same variant would be even better!
Could you please note in the documentation that the the ref/alt alleles need to be harmonized across studies? If the input VCF files are not harmonized, apparently APEX will not recognize the variant as shared across studies and therefore won't include the variant in the meta-analysis. Alternatively, a fix so APEX recognizes flipped ref/alt and alt/ref alleles as the same variant would be even better!