Calculation of PQ and TP values

KatherineSKatherineS Posts: 9Member
edited August 2012 in Ask the GATK team

Dear GATK team,

I'd like to be able to work through the calculations for the PQ (ReadBackedPhasing) and TP (PhaseByTransmission) values for small toy data sets. Is there an article or document anywhere that describes the algorithms used to calculate PQ and TP? Unfortunately I'm only a beginner at Java, so can't answer my questions by looking at the source code.

Thanks for all the great work you do with the GATK.

Best wishes,

Katherine

Answers

  • ebanksebanks Posts: 684GATK Developer mod

    I've just asked the authors of these tools to respond (but it may take some time as neither is affiliated with our group).

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

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