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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Multi-tumor variant calling with Mutect2 (GATK v220.127.116.11) 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.