{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/801","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/801/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/801/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/801/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/801","id":63928962,"number":801,"title":"import into gemini fails for some variants","user":{"login":"parlar","id":7408977,"avatar_url":"https://avatars.githubusercontent.com/u/7408977?v=3","gravatar_id":"","url":"https://api.github.com/users/parlar","html_url":"https://github.com/parlar","followers_url":"https://api.github.com/users/parlar/followers","following_url":"https://api.github.com/users/parlar/following{/other_user}","gists_url":"https://api.github.com/users/parlar/gists{/gist_id}","starred_url":"https://api.github.com/users/parlar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/parlar/subscriptions","organizations_url":"https://api.github.com/users/parlar/orgs","repos_url":"https://api.github.com/users/parlar/repos","events_url":"https://api.github.com/users/parlar/events{/privacy}","received_events_url":"https://api.github.com/users/parlar/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-03-24T07:57:56Z","updated_at":"2015-04-09T14:55:30Z","closed_at":null,"body":"I upgraded to bcbio-nextgen,0.8.8a0-b2fb8ba from 0.8.4. Now the import of variants into gemini sometimes fails. The variant is there (chr/start/end/ref/alt) but gene symbol, impact, ref transcript and perhaps other fields are empty (=None). Most of the imported variants seem ok, however.\r\n\r\nI also noted an example where the genotype field was incorrect (ref = A, alt = AAAC but gt = AAAC|AAAC).\r\n\r\nKind regards,\r\n\r\nPär\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/91254676","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/801#issuecomment-91254676","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/801","id":91254676,"user":{"login":"parlar","id":7408977,"avatar_url":"https://avatars.githubusercontent.com/u/7408977?v=3","gravatar_id":"","url":"https://api.github.com/users/parlar","html_url":"https://github.com/parlar","followers_url":"https://api.github.com/users/parlar/followers","following_url":"https://api.github.com/users/parlar/following{/other_user}","gists_url":"https://api.github.com/users/parlar/gists{/gist_id}","starred_url":"https://api.github.com/users/parlar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/parlar/subscriptions","organizations_url":"https://api.github.com/users/parlar/orgs","repos_url":"https://api.github.com/users/parlar/repos","events_url":"https://api.github.com/users/parlar/events{/privacy}","received_events_url":"https://api.github.com/users/parlar/received_events","type":"User","site_admin":false},"created_at":"2015-04-09T14:55:30Z","updated_at":"2015-04-09T14:55:30Z","body":"Sorry for leaving this hanging, I've had too much to do lately. I'll take a closer look at this asap."}}