{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/oncotator/issues/313","labels_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/313/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/313/comments","events_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/313/events","html_url":"https://github.com/broadinstitute/oncotator/issues/313","id":83617942,"number":313,"title":"M2 VCF to MAF conversion needs a command line and functionality to support it","user":{"login":"LeeTL1220","id":2152339,"avatar_url":"https://avatars.githubusercontent.com/u/2152339?v=3","gravatar_id":"","url":"https://api.github.com/users/LeeTL1220","html_url":"https://github.com/LeeTL1220","followers_url":"https://api.github.com/users/LeeTL1220/followers","following_url":"https://api.github.com/users/LeeTL1220/following{/other_user}","gists_url":"https://api.github.com/users/LeeTL1220/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeTL1220/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeTL1220/subscriptions","organizations_url":"https://api.github.com/users/LeeTL1220/orgs","repos_url":"https://api.github.com/users/LeeTL1220/repos","events_url":"https://api.github.com/users/LeeTL1220/events{/privacy}","received_events_url":"https://api.github.com/users/LeeTL1220/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/oncotator/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":{"login":"LeeTL1220","id":2152339,"avatar_url":"https://avatars.githubusercontent.com/u/2152339?v=3","gravatar_id":"","url":"https://api.github.com/users/LeeTL1220","html_url":"https://github.com/LeeTL1220","followers_url":"https://api.github.com/users/LeeTL1220/followers","following_url":"https://api.github.com/users/LeeTL1220/following{/other_user}","gists_url":"https://api.github.com/users/LeeTL1220/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeTL1220/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeTL1220/subscriptions","organizations_url":"https://api.github.com/users/LeeTL1220/orgs","repos_url":"https://api.github.com/users/LeeTL1220/repos","events_url":"https://api.github.com/users/LeeTL1220/events{/privacy}","received_events_url":"https://api.github.com/users/LeeTL1220/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/broadinstitute/oncotator/milestones/4","html_url":"https://github.com/broadinstitute/oncotator/milestones/Cloaker","labels_url":"https://api.github.com/repos/broadinstitute/oncotator/milestones/4/labels","id":874527,"number":4,"title":"Cloaker","description":"Updates for M2 support","creator":{"login":"alexramos","id":2365065,"avatar_url":"https://avatars.githubusercontent.com/u/2365065?v=3","gravatar_id":"","url":"https://api.github.com/users/alexramos","html_url":"https://github.com/alexramos","followers_url":"https://api.github.com/users/alexramos/followers","following_url":"https://api.github.com/users/alexramos/following{/other_user}","gists_url":"https://api.github.com/users/alexramos/gists{/gist_id}","starred_url":"https://api.github.com/users/alexramos/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alexramos/subscriptions","organizations_url":"https://api.github.com/users/alexramos/orgs","repos_url":"https://api.github.com/users/alexramos/repos","events_url":"https://api.github.com/users/alexramos/events{/privacy}","received_events_url":"https://api.github.com/users/alexramos/received_events","type":"User","site_admin":false},"open_issues":3,"closed_issues":0,"state":"open","created_at":"2014-11-20T17:07:17Z","updated_at":"2015-06-03T17:46:10Z","due_on":"2016-06-07T04:00:00Z","closed_at":null},"comments":6,"created_at":"2015-06-01T17:39:56Z","updated_at":"2015-06-05T12:57:36Z","closed_at":null,"body":"- ``TLOD`` (INFO) needs to be rendered as ``t_lod_fstar`` (not to be confused with the filter of the same name).\r\n- ``--collapse-filter-cols`` must be specified!  This needs to go into Firehose.\r\n- ``--skip-no-alt`` must be specified.\r\n- ``AF`` (FORMAT) needs to be called tumor_f.\r\n- ``AD`` annotation is comma separated (ref,alt), but in the MAF needs to be rendered as two separate values with (``t_ref_count`` and ``t_alt_count``).  Could also be array indexes, if need be (e.g. AD[0]).\r\n- ``i_t_ALT_F2R1`` (and similar 4 total) needs to be emitted and M2 will produce the corresponding ``ALT_F2R1`` (and similar 4 total)\r\n\r\n\r\nNeed to specify final command line and any code changes to support M2 VCFs being converted into MAFs that look like the ones in the current CGA FH workflow. \r\n\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/oncotator/issues/comments/109284616","html_url":"https://github.com/broadinstitute/oncotator/issues/313#issuecomment-109284616","issue_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/313","id":109284616,"user":{"login":"LeeTL1220","id":2152339,"avatar_url":"https://avatars.githubusercontent.com/u/2152339?v=3","gravatar_id":"","url":"https://api.github.com/users/LeeTL1220","html_url":"https://github.com/LeeTL1220","followers_url":"https://api.github.com/users/LeeTL1220/followers","following_url":"https://api.github.com/users/LeeTL1220/following{/other_user}","gists_url":"https://api.github.com/users/LeeTL1220/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeTL1220/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeTL1220/subscriptions","organizations_url":"https://api.github.com/users/LeeTL1220/orgs","repos_url":"https://api.github.com/users/LeeTL1220/repos","events_url":"https://api.github.com/users/LeeTL1220/events{/privacy}","received_events_url":"https://api.github.com/users/LeeTL1220/received_events","type":"User","site_admin":false},"created_at":"2015-06-05T12:57:36Z","updated_at":"2015-06-05T12:57:36Z","body":"@kcibul @ldgauthier FYI... ``tumor_f`` will only come out when using ``-o TCGAMAF`` (the default and what will be the recommended standard for producing M2 MAFs)  I doubt this piece of information will ever matter, but I am mentioning it here."}}