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Multi-tumor variant calling with Mutect2 (GATK v22.214.171.124) weakens sensitivity
This observation is very clear when one or more of the tumor samples have very low tumor content or no tumor content.
So for example if we have tumor1 and tumor2 with high tumor content and tumor3 with low tumor content, using Mutect2 on tumor1 and tumor2 will produce a lot more variants than when doing the calling on tumor1, tumor2 and tumor3 together.