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Calculating family prior

Kelly135Kelly135 KoreaMember
edited February 2016 in Ask the GATK team

https://www.broadinstitute.org/gatk/guide/article?id=4726

I have a question regarding family prior in the article on the link above. There are two numbers 10 and two when no MV, and I wonder where these numbers come from.

  1. Calculation of Family Priors
    Given a genotype configuration for a given mother, father, and child trio, we set the prior probability of that genotype configuration as follows:

P(GM,GF,GC)=P(G⃗ )⎧⎩⎨1−10μ−2μ2μμ2 no MV 1 MV 2 MVs
P(GM,GF,GC)=P(G→){1−10μ−2μ2 no MV μ 1 MV μ2 2 MVs
where the 10 configurations with a single Mendelian violation are penalized by the de novo mutation probability μ and the two configurations with two Mendelian violations by μ^2. The remaining configurations are considered valid and are assigned the remaining probability to sum to one.

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