I think this is relevant to this thread, which is why I'm reawakening it:
According to 1000genomes's VCF 4.1 spec, the ordering of genotypes is given by this:
Just in case anyone else is desperately googling for the answer to how to order genotypes for bi/triallelic alternate alleles in a vcf file!
According to 1000genomes's VCF 4.1 spec, the ordering of genotypes is given by this:
If A is the allele in REF and B,C,... are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc.
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