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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.