UPDATE: 7/20/2018 - Added links and updated name for coverageReporters.
UPDATE: 8/14/2017 - This answer is totally outdated. Just look at the Jest docs now. They have official support and documentation about how to do this.
@hankhsiao has got a forked repo where Istanbul is working with Jest.  Add this to your dev dependencies
 "devDependencies": {
     "jest-cli": "git://github.com/hankhsiao/jest.git"
 }
Also make sure coverage is enabled in your package.json jest entry and you can also specify formats you want.  (The html is pretty bad ass).
 "jest": {
     "collectCoverage": true,
     "coverageReporters": ["json", "html"],
 }
See Jest documentation for coverageReporters (default is  ["json", "lcov", "text"])
Or add --coverage when you invoke jest.