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Somatic variant calling using Mutect2 --- normal reference is the genomes of two people
Dear GATK team,
We have data from a cancer patient who had bone marrow transplant from his sister. Now we have the WGS data from the patient's tumor tissue and his and his sister's normal tissues.
We wonder if we could pool WGS data from his and his sister's normal tissues together as the new "normal" reference and then run Mutect2?
I noticed that in the Mutect2 white paper, there is an assumption that the normal reference is diploid. That's why I ask the above question.