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.
Could I use variantEval to evaluate somatic mutation calling by mutect2?
I have a basic question about VariantEval? could I use this methods to evaluate somatic mutation from tumor? I tried with default parameter: even there are more than 40K lines mutations passed filter, VariantEvalonly report about 1K variants in the callset. I am trying to understand why VariantEval get so few, what is the filter VariantEval use? How do I tell how these mutations are filtered out by VariantEval?
Thanks a lot for help,