{"action":"created","issue":{"url":"https://api.github.com/repos/hail-is/hail/issues/803","repository_url":"https://api.github.com/repos/hail-is/hail","labels_url":"https://api.github.com/repos/hail-is/hail/issues/803/labels{/name}","comments_url":"https://api.github.com/repos/hail-is/hail/issues/803/comments","events_url":"https://api.github.com/repos/hail-is/hail/issues/803/events","html_url":"https://github.com/hail-is/hail/issues/803","id":177684481,"number":803,"title":"question: what does \"Variant is symbolic\" mean?","user":{"login":"bw2","id":6240170,"avatar_url":"https://avatars.githubusercontent.com/u/6240170?v=3","gravatar_id":"","url":"https://api.github.com/users/bw2","html_url":"https://github.com/bw2","followers_url":"https://api.github.com/users/bw2/followers","following_url":"https://api.github.com/users/bw2/following{/other_user}","gists_url":"https://api.github.com/users/bw2/gists{/gist_id}","starred_url":"https://api.github.com/users/bw2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bw2/subscriptions","organizations_url":"https://api.github.com/users/bw2/orgs","repos_url":"https://api.github.com/users/bw2/repos","events_url":"https://api.github.com/users/bw2/events{/privacy}","received_events_url":"https://api.github.com/users/bw2/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-09-18T23:22:49Z","updated_at":"2016-09-21T02:25:02Z","closed_at":null,"body":"I'm seeing this warning for ~0.1% of variants:\r\n\r\ncase Symbolic => \"Variant is symbolic\"  \r\n\r\njust curious what it means.\r\n"},"comment":{"url":"https://api.github.com/repos/hail-is/hail/issues/comments/248493285","html_url":"https://github.com/hail-is/hail/issues/803#issuecomment-248493285","issue_url":"https://api.github.com/repos/hail-is/hail/issues/803","id":248493285,"user":{"login":"cseed","id":1244990,"avatar_url":"https://avatars.githubusercontent.com/u/1244990?v=3","gravatar_id":"","url":"https://api.github.com/users/cseed","html_url":"https://github.com/cseed","followers_url":"https://api.github.com/users/cseed/followers","following_url":"https://api.github.com/users/cseed/following{/other_user}","gists_url":"https://api.github.com/users/cseed/gists{/gist_id}","starred_url":"https://api.github.com/users/cseed/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cseed/subscriptions","organizations_url":"https://api.github.com/users/cseed/orgs","repos_url":"https://api.github.com/users/cseed/repos","events_url":"https://api.github.com/users/cseed/events{/privacy}","received_events_url":"https://api.github.com/users/cseed/received_events","type":"User","site_admin":false},"created_at":"2016-09-21T02:25:02Z","updated_at":"2016-09-21T02:25:02Z","body":"Symbolic variants are defined in the VCF spec.  They are for specifying imprecise structural variation.  They should be defined in the header file like this:\r\n\r\n```\r\n##ALT=<ID=type,Description=description>\r\n```\r\n\r\nand then appear in the ALT field something like:\r\n\r\n```\r\n20 17330 . T A,<type> ...\r\n```\r\n\r\nSee VCF v4.2 sections 1.2.5 and 1.4.1(4).\r\n\r\nRight now we don't have a way to represent them in Hail so we are filtering them out.  Where is your VCF from?  As far as I know GATK doesn't generate them, but I think they are generated by other tools, e.g., Genome STRiP."}}
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