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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.
Estimating error/mismatch rate by Mutect2
So finally Mutect2 calls variants from multiple tumors, and it's great (at least the SNVs). Now assume we have tumorA and tumorB (from the same individual), and Mutect2 calls a variant in tumorA (high allele fraction), but tumor 2 has only 1-2 reads supporting the variant allele. To be able to decide whether the variant in tumorB exists, we need to estimate the mismatch/error rate, and compare the 1-2 reads seen in tumorB with the expected error rate. We can in general estimate the mismatch rate using Picard CollectAlignmentSummaryMetrics, but the numbers don't seem to reflect the real error rate emitted by Mutect2, likely because Mutect2 applies its own read filters beforehand.
Is there a tool/trick to get the background error rate under Mutect2 filters?