bam2mpg calls genotypes from sequence reads of haploid or diploid DNA aligned to a closely-related reference sequence. The program reads alignments in BAM format (http://samtools.sourceforge.net). The MPG (Most Probable Genotype) algorithm is based on a Bayesian model which simulates sampling from one or two alleles with sequencing error, and then calculates the likelihood of each possible genotype given the observed sequence data. Using prior probabilities dependent on the expected heterozygosity of the sequence, MPG then predicts the “Most Probable Genotype” at each site, along with quality scores estimating the accuracy of the calls.
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