{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/gemini/issues/415","labels_url":"https://api.github.com/repos/arq5x/gemini/issues/415/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/gemini/issues/415/comments","events_url":"https://api.github.com/repos/arq5x/gemini/issues/415/events","html_url":"https://github.com/arq5x/gemini/issues/415","id":64620393,"number":415,"title":"Issue with new snpEff annotations in classic mode","user":{"login":"dgaston","id":1605762,"avatar_url":"https://avatars.githubusercontent.com/u/1605762?v=3","gravatar_id":"","url":"https://api.github.com/users/dgaston","html_url":"https://github.com/dgaston","followers_url":"https://api.github.com/users/dgaston/followers","following_url":"https://api.github.com/users/dgaston/following{/other_user}","gists_url":"https://api.github.com/users/dgaston/gists{/gist_id}","starred_url":"https://api.github.com/users/dgaston/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dgaston/subscriptions","organizations_url":"https://api.github.com/users/dgaston/orgs","repos_url":"https://api.github.com/users/dgaston/repos","events_url":"https://api.github.com/users/dgaston/events{/privacy}","received_events_url":"https://api.github.com/users/dgaston/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":12,"created_at":"2015-03-26T20:04:02Z","updated_at":"2015-03-27T18:32:54Z","closed_at":null,"body":"Even in -classic and -formatEff the new snpEff (4.1) has changed SPLICE_SITE_REGION to SPLICE_SITE_REGION+INTRON which prevents parsing of the snpeff effects for these sites by GEMINI"},"comment":{"url":"https://api.github.com/repos/arq5x/gemini/issues/comments/87045369","html_url":"https://github.com/arq5x/gemini/issues/415#issuecomment-87045369","issue_url":"https://api.github.com/repos/arq5x/gemini/issues/415","id":87045369,"user":{"login":"dgaston","id":1605762,"avatar_url":"https://avatars.githubusercontent.com/u/1605762?v=3","gravatar_id":"","url":"https://api.github.com/users/dgaston","html_url":"https://github.com/dgaston","followers_url":"https://api.github.com/users/dgaston/followers","following_url":"https://api.github.com/users/dgaston/following{/other_user}","gists_url":"https://api.github.com/users/dgaston/gists{/gist_id}","starred_url":"https://api.github.com/users/dgaston/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dgaston/subscriptions","organizations_url":"https://api.github.com/users/dgaston/orgs","repos_url":"https://api.github.com/users/dgaston/repos","events_url":"https://api.github.com/users/dgaston/events{/privacy}","received_events_url":"https://api.github.com/users/dgaston/received_events","type":"User","site_admin":false},"created_at":"2015-03-27T18:32:54Z","updated_at":"2015-03-27T18:32:54Z","body":"I agree absolutely that just updating to a newer version of snpEff is the best solution long term. Putting some notice in the current documentation about the issue would probably be a good bet so people know. You can easily pull all of these variants by querying for \"impact_sevierity is NULL\" as a SQL where clause."}}