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.
ML estimator with known minor
First infer the Major and Minor allele and then use BFGS (-doMaf 1) optimazation or the EM algorithm (-doMaf 2) to estimate the allele frequencies.
ML estimator with unknown minor
First infer the Major allele and then use BFGS (-doMaf 4) optimazation or the EM algorithm (-doMaf 8) to estimate the allele frequencies. Here only the Major allele needs to be known and the uncertaincy of infering the minor allele is modelled.
Let denote the major an minor allele assuming adiallelic site, then the maximum likelihood estimate of this pair is found using the likelihood function