ANGSD: Analysis of next generation Sequencing Data
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Error estimation method
The estimated rates can roughly be intrepreted as relative error rates. That is excess of errors in your sample compare to the error in the perfect indviduals. The idea is the your sample and the perfect individuals should have the same expected number of derived alleles and the extra derived alleles in you sample are due to the excess errorr. For each individual we sample a single base from the reads at each position. We use only positions were there are coverage for both the chimp, the sample and the perfect man. The overall error rate is obtained from
were
is the error rate
is the observed number of derived alleles in the sample
is the expected number of derived alleles which is obtained from the observed derived alleles from the perfect man
is the expected number of ancestral alleles which is obtained from the perfect man
For the type specific error rates are obtained from maximizing the likehood
where
is the allele of you sample
is the allele of the chimp
is the error rate for base a to base b
are obtained from the perfect man assuming that the perfect man has no errors.