Question

Visualization Of Mutect Output For Point Mutation Detection

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11.7 years ago

jeremy ▴ 80

The mutation call output of MuTect from Broad is not a standard format that can be loaded into IGV. Does anyone know any tool that can visulizae MuTect output, or tools that can convert MuTect output into .VCF format or .MUT format, which can be loaded into IGV for visulization?

mutation • 3.5k views

ADD COMMENT • link updated 11.7 years ago by Malachi Griffith 20k • written 11.7 years ago by jeremy ▴ 80

score 1 · Answer 1 · 2013-03-18

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11.7 years ago

henryvuong ▴ 810

MuTect (1.1.4) can output vcf file directly

ADD COMMENT • link 11.7 years ago by henryvuong ▴ 810

score 0 · Answer 2 · 2013-02-27

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11.7 years ago

Chris Miller 22k

I'm not familiar with the MuTect format, but IGV will load bed files happily (chr, start, stop, name - ie. chr1 1234 1235 A/T) I have to imagine some form of that info is the mutect output that you could munge into a bed file.

ADD COMMENT • link 11.7 years ago by Chris Miller 22k