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Haplotype Scoring Algorithm

priesgopriesgo PanamáMember Posts: 22
edited November 2012 in Ask the GATK team

Hi there,

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!

Post edited by Geraldine_VdAuwera on

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,130 admin
  • priesgopriesgo PanamáMember Posts: 22


    Thanks for your answer.
    They are not really talking about haplotype scoring algorithm in that article. Anyway that lead me to the fragment-based SNP calling slides and they are referring to an "e" which is the sequencing error rate. May it be this?
    We had ei, so it would be specific to that position and not a static sequencing error. I guess it is the error rate for position i in haplotype j, that might be the number of mismatches to consensus haplotype j at position i over the total counts for position i at haplotype j.

    But I still doubt how are you calculating the error sequencing rate? Going through the documentation for ErrorRatePerCycle, the error sequencing rates calculated there do not match only to mismatches/counts.


  • priesgopriesgo PanamáMember Posts: 22

    Aaaaaaahhhh, OK. I knew it had to be something evident... that makes sense.
    I just wanted to fully understand the haplotype scoring and I missed what this e was, I was thinking about calculating some error probability

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