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I'm trying to understand the haplotype scoring algorithm in GATK 1.6.5. I fortunately got a printed page where I have a simple diagram that explains the algorithm, I can't find it anymore in the new web. The case is that the formula for calculating the haplotype score in this diagram has a variable that I'am missing what it is. This is the formula as it's written:
P(read | haplotype_j) = sum_bi (bi == hi ? ei : 1 - ei / 3) - sum_bi (ei)
I guess bi stands for base at position i at the current read and hi stands base at position i at haplotype_j, that makes sense for me. But, what is ei?? maybe I'm missing something... it looks like it should be a probability in the range (0, 1) for the haplotype score to make sense.
Thanks in advance! Pablo.