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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.
Are there any plans for MuTect to output its results as a VCF file? Like many other bioinformaticians, a lot of my current tool-chain is built around VCFs output by the GATK, including the critical annotation steps.
I'm really interested in using MuTect, but the lack of VCF output represents a not-insignificant hurdle to overcome, even in comparing the calls made by MuTect against other callers. I'll happily write some scripts to parse MuTect output into VCF, but thought I should ask first if I was being naive or if MuTect->VCF scripts already existed.