So I've finished running my analysis for Mutect 2. My main question is this. When I ran this analysis Mutect found lets say 250 possible mutations in my tumor with pair normal. However when I run the same with just the tumor sample I get considerable more mutations. Its in the 7600s. Is this normal or am I doing something wrong? The way the final analysis is set up is the vcf is displayed when the chr that is mutated in at least two or more samples.
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