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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.
GATK vs MuTect2
first question, which is better to use on unmatched cancer samples (no normal panel either), MuTect or GATK?
second, I ran GATK on two samples (pair), for which there was a different list of mutations. However, when I ran MuTect on the pair, the list i got did not include the differences that GATK picked up. In other words, if there's a mutation that GATK could detect in one but not the other, it means the allele frequency was different. So MuTect should be able to pick it up with it's hypothesis testing.