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Hi there,

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?

Best regards,


Best Answer


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