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Detailed Statistical Model of UnifiedGenotyper?

CindyCindy Member Posts: 19

Hi there,

I am interested in the details of UnifiedGenotyper's statistical model. I came across GATKPaperGenotyper and was told that the statistical model applied there is not feasible for applying it to real-world data. Nevertheless, I am interested how the UnifiedGenotyper now works in detail, since I originally thought that GATKPaperGenotyper's model would have been applied by the UnifiedGenotyper. I cannot find any other documentation than from code (which is unfortunately not very detailed, and the code itself not being that expressive) except for this slide: http://www.broadinstitute.org/gatk/guide/article?id=1237

Unfortunately, I cannot find how P(b|G) is exactly calculated or what aspects are considered for calculation of P(G) and P(D|G)...

Any explanations, recommendations, or further references would be very appreciated!

Best regards,

Cindy

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