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GATK vs MuTect2

afaddaafadda Member

first question, which is better to use on unmatched cancer samples (no normal panel either), MuTect or GATK?
second, I ran GATK on two samples (pair), for which there was a different list of mutations. However, when I ran MuTect on the pair, the list i got did not include the differences that GATK picked up. In other words, if there's a mutation that GATK could detect in one but not the other, it means the allele frequency was different. So MuTect should be able to pick it up with it's hypothesis testing.

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