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!
I don't know if this question has been asked, if so sorry.
When using UnifiedGenotyper, I was wondering if it was possible (via hidden command option, etc) to use a VCF file as a prior. Currently I have just been adding additional bam files, but it would be nice (and quicker) if I could use a Indexed file.
Thanks for your time.