ANGSD: Analysis of next generation Sequencing Data

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# SYKmaf

From angsd

Revision as of 19:50, 15 December 2014 by Albrecht (talk | contribs) (Undo revision 2344 by Albrecht (talk))

## 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