{"action":"created","issue":{"url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/issues/43","labels_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/issues/43/labels{/name}","comments_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/issues/43/comments","events_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/issues/43/events","html_url":"https://github.com/NationalGenomicsInfrastructure/piper/issues/43","id":50359965,"number":43,"title":"Add snpEff","user":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2014-11-28T10:21:27Z","updated_at":"2015-01-08T12:54:27Z","closed_at":null,"body":"It would be great if we could get GATK to run snpEff by adding the `-o gatk` (see the [snpEff documentation](http://snpeff.sourceforge.net/))\r\n\r\nThis is fairly urgent as the report scripts look for the snpEff output. Tack!"},"comment":{"url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/issues/comments/69175324","html_url":"https://github.com/NationalGenomicsInfrastructure/piper/issues/43#issuecomment-69175324","issue_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/issues/43","id":69175324,"user":{"login":"johandahlberg","id":1788862,"avatar_url":"https://avatars.githubusercontent.com/u/1788862?v=3","gravatar_id":"","url":"https://api.github.com/users/johandahlberg","html_url":"https://github.com/johandahlberg","followers_url":"https://api.github.com/users/johandahlberg/followers","following_url":"https://api.github.com/users/johandahlberg/following{/other_user}","gists_url":"https://api.github.com/users/johandahlberg/gists{/gist_id}","starred_url":"https://api.github.com/users/johandahlberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/johandahlberg/subscriptions","organizations_url":"https://api.github.com/users/johandahlberg/orgs","repos_url":"https://api.github.com/users/johandahlberg/repos","events_url":"https://api.github.com/users/johandahlberg/events{/privacy}","received_events_url":"https://api.github.com/users/johandahlberg/received_events","type":"User","site_admin":false},"created_at":"2015-01-08T12:54:27Z","updated_at":"2015-01-08T12:54:27Z","body":"Have you've been using the `snpEff_summary.html` to extract info for the reports or do you want me to run with the `-csvStats` option?"}}