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Mutect1 multi-allelic cases
We have worked hard to figure this out.
By default, or by using any parameters, Mutect1 does not catch multi-allelic cases at a single position. It seems to pick one of the alternate alleles at every position (randomly?). As in mutect2, one expects ploidy like parameter. We need to detect every alternate allele at that position, as somatic analysis requires this.
Do you have an idea? How should one use Mutect1 for detecting multiallelic cases?