{"action":"opened","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1125","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1125/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1125/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1125/events","html_url":"https://github.com/broadinstitute/gatk/issues/1125","id":117218559,"number":1125,"title":"ApplyBQSR ignores useOriginalQualities","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-11-16T21:10:19Z","updated_at":"2015-11-16T21:10:19Z","closed_at":null,"body":"in GATK3 useOriginalQualities is an engine level argument. In hellendender, it's only used in BaseRecalibrator and so you can't applyBQSR on originalBase qualities.\r\n\r\n@eitanbanks is this an alpha requirement? "}}