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Outputting REF calls in Mutect
Hi. I wonder if there's any way to output REF calls with MuTect, so that I can distinguish them from no-calls? What I'd like to obtain is a confidence-score for ref calls, i.e.
Here's the background. My goal is to apply MuTect (1.1.7) to a bunch of different samples and combine the outputs site-by-site. However, if MuTect doesn't call a site in a given sample, I don't see any way of telling if that was because
1. MuTect thinks the site is REF
2. the quality at the site is too poor for MuTect to tell, one way or the other.
I understand that it would be impracticable for MuTect to output every single REF call, but perhaps it could so if I gave it a bedfile of specific sites to look at. Or maybe another tool like HaplotypeCaller/mpile would be better suited for this? Or maybe there's some functionality in MuTect that I'm completely missing?
Thanks for any help you can offer.