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Tools alpha-3 release","description":"#### CNV (Germline and Somatic)\r\n- New coverage model\r\n\r\n#### WGS\r\n- Evaluation of GATK CNV for WGS\r\n- ACNV for WGS\r\n- Evaluation of GATK ACNV for WGS\r\n- GC correction and eval in WGS \r\n\r\n#### Other\r\n- WDL\r\n","creator":{"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},"open_issues":35,"closed_issues":31,"state":"open","created_at":"2016-03-02T15:52:34Z","updated_at":"2016-07-07T13:41:25Z","due_on":"2016-07-30T04:00:00Z","closed_at":null},"comments":1,"created_at":"2016-07-07T13:41:25Z","updated_at":"2016-07-07T13:46:40Z","closed_at":null,"body":""},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/comments/231082051","html_url":"https://github.com/broadinstitute/gatk-protected/issues/604#issuecomment-231082051","issue_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/604","id":231082051,"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":"2016-07-07T13:46:40Z","updated_at":"2016-07-07T13:46:40Z","body":"An input file should be a tsv with tumor + normal sample information:\r\nExample input file (should be tab-delimited):\r\n```\r\nT1 T1_bam_path N1 N1_bam_path\r\nT2 T2_bam_path N2 N2_bam_path\r\n```\r\n\r\nExample wdl to parse the tsv:\r\n\r\n```\r\nworkflow {\r\n...\r\n  File input_file_list\r\n  Array[Array[File]] file_list_array = read_tsv(input_file_list)\r\n...\r\n\r\n  scatter (row in file_list_array) {\r\n        call some_task_name_here {\r\n            input:\r\n                t_entity_id=row[0],\r\n                t_bam_file=row[1],\r\n                n_entity_id=row[2],\r\n                n_bam_file=row[3]\r\n        }\r\n  }\r\n...\r\n}\r\n```"}}
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