I am running mutect 1.1.7 and mutect2 (GATK 3.7) on tumor/normal paired samples and compare results between the two, the overlap are usually very good at ~90%. But I got poor overlap ( <20%) for a data set I am working on recently. I did not change any thing when I ran mutect and mutect2. I assume it must be the data which cause the problems, but what kind of data could cause poor overlap between mutect and mutect2?
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