{"action":"created","issue":{"url":"https://api.github.com/repos/ucscCancer/varscan-tool/issues/1","labels_url":"https://api.github.com/repos/ucscCancer/varscan-tool/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/ucscCancer/varscan-tool/issues/1/comments","events_url":"https://api.github.com/repos/ucscCancer/varscan-tool/issues/1/events","html_url":"https://github.com/ucscCancer/varscan-tool/pull/1","id":102817044,"number":1,"title":"Wrap VarScan","user":{"login":"ernfrid","id":397990,"avatar_url":"https://avatars.githubusercontent.com/u/397990?v=3","gravatar_id":"","url":"https://api.github.com/users/ernfrid","html_url":"https://github.com/ernfrid","followers_url":"https://api.github.com/users/ernfrid/followers","following_url":"https://api.github.com/users/ernfrid/following{/other_user}","gists_url":"https://api.github.com/users/ernfrid/gists{/gist_id}","starred_url":"https://api.github.com/users/ernfrid/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ernfrid/subscriptions","organizations_url":"https://api.github.com/users/ernfrid/orgs","repos_url":"https://api.github.com/users/ernfrid/repos","events_url":"https://api.github.com/users/ernfrid/events{/privacy}","received_events_url":"https://api.github.com/users/ernfrid/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-08-24T15:16:27Z","updated_at":"2015-08-30T23:01:31Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ucscCancer/varscan-tool/pulls/1","html_url":"https://github.com/ucscCancer/varscan-tool/pull/1","diff_url":"https://github.com/ucscCancer/varscan-tool/pull/1.diff","patch_url":"https://github.com/ucscCancer/varscan-tool/pull/1.patch"},"body":"This is an attempt to fix TCGA validation errors by running VarScan through a wrapper. I also attempted to update the XML file. Please let me know if you run into any problems or notice any part of this that looks problematic or incorrect. I have tested on chr21 for a test BAM."},"comment":{"url":"https://api.github.com/repos/ucscCancer/varscan-tool/issues/comments/136213059","html_url":"https://github.com/ucscCancer/varscan-tool/pull/1#issuecomment-136213059","issue_url":"https://api.github.com/repos/ucscCancer/varscan-tool/issues/1","id":136213059,"user":{"login":"jacmarjorie","id":6373975,"avatar_url":"https://avatars.githubusercontent.com/u/6373975?v=3","gravatar_id":"","url":"https://api.github.com/users/jacmarjorie","html_url":"https://github.com/jacmarjorie","followers_url":"https://api.github.com/users/jacmarjorie/followers","following_url":"https://api.github.com/users/jacmarjorie/following{/other_user}","gists_url":"https://api.github.com/users/jacmarjorie/gists{/gist_id}","starred_url":"https://api.github.com/users/jacmarjorie/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jacmarjorie/subscriptions","organizations_url":"https://api.github.com/users/jacmarjorie/orgs","repos_url":"https://api.github.com/users/jacmarjorie/repos","events_url":"https://api.github.com/users/jacmarjorie/events{/privacy}","received_events_url":"https://api.github.com/users/jacmarjorie/received_events","type":"User","site_admin":false},"created_at":"2015-08-30T23:01:30Z","updated_at":"2015-08-30T23:01:30Z","body":"\"FORMAT value 'GT:GQ:DP:RD:AD:FREQ:DP4' is not valid. The following mandatory format fields are missing: BQ,SS\"\r\n\r\nhas now changed to a report that:\r\n\r\n\"FORMAT value 'GT:GQ:DP:RD:AD:FREQ:DP4:BQ:SS' is not valid. Format data contains a field that has not been defined in the headers: 'BQ'\" as well as \"VCF data validation error on line 23: INFO value 'SS' is not valid. ID not defined in headers\".\r\n\r\nThere could potentially be more, but the program haults after alternating back and forth between these two errors for 120 lines in the vcf. This is happening for both the indel and the snp file."}}