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I just walked a bit through GATK code and came across the class org.broadinstitute.sting.gatk.examples.GATKPaperGenotyper. The comments state that this genotyper is only intended to be used as example in the GATK paper and that it uses a much simpler model for calling than UnifiedGenotyper.
At first glance, this genotyper seems to apply the methods I thought GATK's UnifiedGenotyper would use in general (heterozygosity values for prior probability and using the base quality scores for genotype likelihood). So now I am interested in what way this simple genotyper differs from the strategies used in the actual tool - what other factors are considered in UnifiedGenotyper's statistical model? Up to now I could not figure out the actual differences to UnifiedGenotyper from just browsing through its code...
And what is more, how applicable is the simpler model for SNP calling in practice?