snpprobs

[kidd...@gmail.com]

Hello Karl,

I was wondering what the reason was for coding snpprobs as a two columns for the probability of the two possibilities (A/B) when calculated using allele probabilities rather than just having a single probability for "A" since B would be 1 - prob of A if I understand the idea correctly.

Cheers

Senthil

[Karl Broman]

We treat the SNP probabilities as a special case of the general multi-allelic probabilities. And SNP probabilities could be for genotypes AA,AB,BB, or just for alleles A,B.

There's no particularly reason. We'd save memory by dropping the last column, but some aspects of the software would be more complicated.

karl