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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.

Can one get bamout for the normal sample in Mutect2?

Is it possible to get a bamout for the normal sample in Mutect2? Is the local realignment performed also for the normal sample? I have several case samples where I get variants (exactly the same variant in several different case samples) called that I can also see when visualizing using igv in high frequency the normal bam but only in reads with zero mapping quality. I would like to understand what goes wrong.



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