Post by lhooq on Jul 8, 2015 21:37:24 GMT
Does GCTA have capability to deal with sites that have more than three genotypes? Specifically, bi-allelic sites {AA,AG,GG} are clearly supported, but what about multi allelic sites? I tried a mocked up a test genotype file with three alleles, and the algorithm didn't fail, but there was no reference to the third allele in the output. Are alleles beyond the two most common alleles simply treated as missing?