{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/950","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/950/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/950/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/950/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/950","id":97955076,"number":950,"title":"Export chanjo coverage file","user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-07-29T14:53:31Z","updated_at":"2015-07-29T15:11:52Z","closed_at":null,"body":"This is a feature request; I'd appreciate it if the annotated Chanjo coverage BED file could be part of the final `upload` results. I am referring to an unfiltered (!) version of the temporary BED file generated [here](https://github.com/chapmanb/bcbio-nextgen/blob/c45b7cfe069e3703ee44c298fa02de46cee3399c/bcbio/variation/coverage.py#L130). The Chanjo database is much less accessible and requires SQLite to get the same data. I would like to use these data to get at the number of regions with at least 20x (or 1x) sequencing coverage."},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/125984025","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/950#issuecomment-125984025","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/950","id":125984025,"user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"created_at":"2015-07-29T15:11:52Z","updated_at":"2015-07-29T15:11:52Z","body":"Well, Rory, I guess it's your timing that is impeccable then. Thank you. If by any chance you were also interested in 20x coverage ratios, I suggest that these could be added to qcsummary.py - but I can do that in post processing, too. "}}