ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.

Majorminor

From angsd
Revision as of 20:41, 14 June 2012 by Albrecht (talk | contribs) (Created page with "Assuming that the considered site is diallelic, we infer those two alleles using the genotype likelihoods. Let <math>\{M,m\}</math> denote the two possible alleles at the dial...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Assuming that the considered site is diallelic, we infer those two alleles using the genotype likelihoods. Let denote the two possible alleles at the diallelic site, then the maximum likelihood estimate of this pair is found using the likelihood function

where is the genotype likelihood. We then assume that the two alleles within an individual are independent and randomly drawn from the set with equal probability, ignoring the fact that the two alleles at a diallelic site are not observed equally frequent. This gives us for all four possible combinations of . Therefore we estimate the two possible alleles at the diallelic site by

To infer which of these two alleles is the minor allele, we estimate the allele frequencies (only one iteration of the EM algorithm is needed if the starting point is frequencies of 0.5).