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Haplotype phasing somatic mutations from MuTect2 using read-backed phasing and parental data
To whom it may concern,
I have both normal and tumour sample and I also have the parental data (both mother and father) for the patient sample. I hope to first haplotype phase the SNP and INDELs from the haplotype caller using PhaseByTransmission. Thereafter, I wanted to haplotype phase the somatic mutations from MuTect2 using Read-Backed Phasing.
I wanted to ask whether the Read-Backed Phasing method will consider both the SNP and INDEL encompassed within the read and whether it will also consider the information from PhaseByTransmission when haplotype phasing the somatic mutations.