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@Sheila Hi, Thanks for your reply, but I still think the whole changes can be explained using a simplified and beatiful probability structure. I'm sorry to not notice your reply theses days in this post, because I'm waiting for your reply in this p…
@Sheila Hi, Thanks for your reply! And that's where the problem comes, why the two hmms(same in Essentially) named with different names? Is it because the history reason or they are proposed in different author and published in different time? An…
Hi, recently I read the code of haplotypeCaller, and I find that there are two hmm-model in GATK, one in BaseRecalibrator called profile hmm, and one in haplotypeCaller called pair Hmm. I want to know the difference between these two hmms. So, I rea…
@Sheila Hi, thanks for the kind reply. I read the code from here (Quote) And I want to know how to explain this equation using a probabilty structrue or the hierarchicalBayesianQualityEstimate you defined. Any mathematical explaination about this…
Dear GATK team, Recently, I downloaded the code of GATK. And I felt a confused about the algorithm of BQSR. In BaseRecalibrator, I could understand the empirical quality is a MAP of product of the Gaussian prior and the likelihood equivalent to …
Ok, thanks for the kind reply.
Has the paper about algorithms used in Haplotype Caller published?If so could you give me a reference please.Thanks in advance.