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Rationale behind MuTect2 and Haplotype Caller
Dear GATK team,
I would like to better understand MuTect2 and HaplotypeCaller in order to present the methods, as I am doing a Thesis on Somatic Mutation Discovery. Unfortunately the only reference that I have is the original MuTect paper.
First question : Is there any reference that explain how HaplotypeCaller works in detail ? (So it could answer my questions)
I nevertheless have some questions about how the original MuTect is intricated with the HaplotypeCaller.
As far as I understood the HaplotypeCaller use 4 steps (and MuTect2 also I assume?) :
1. Define active regions
2. Determine haplotypes by assembly of the active region
3. Determine likelihoods of the haplotypes given the read data
4. Assign sample genotypes
And as far as I understood, to define the active regions, the original MuTect TLOD is used (and I don't know about the NLOD).
My questions are :
- Are likelihoods calculated with the PairHMM in 3) linked to the TLOD and NLOD ? Is it used to select variants ?
- At the end, what are the parameters that allow to give the "PASS" ? I know there is the TLOD and the NLOD thresholds (I know TLOD>6.3 from the orignal MuTect), but how the steps 2) 3) and 4) are affecting the labelling of a variant as "PASS" ?
Is there any paper on that method that will be released soon ?
Thank you very much in advance ! Have a nice day. Kind regards,