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.
How do MuTect1.1.4 and MuTect2 differ in Tumor only mode (no matched control) variant calling
What is the difference between MuTect1.1.4 and MuTect2 versions in Tumor only mode (no matched control) variant calling method? Is there a preference of using one over the other for this specific application? I would prefer not to use a PON vcf and run tumor only mode to identify variants and use COSMIC/dbSNP to filter out common SNPs. How do I interpret the KEEP vs REJECT calls in this case where there is no matched control to determine somatic variants?