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 am attempting to run GATK's PhasebyTransmission command to phase a vcf file contains a father, mother, son trio generated from complete genomics mkvcf command.
After creating the ped file and running the command I generate the error: "MESSAGE: BUG: Attempted to get likelihoods as strings and neither the vector nor the string is set!". I am not exactly sure what this means.
When I check my file and the documentation I am able to see that the 'GL' field is contained in the file, but could this not be the case? I have attached a few lines from the vcf I am using.
Any help with resolving the this issue would be of great help.