{"action":"opened","issue":{"url":"https://api.github.com/repos/lomereiter/sambamba/issues/146","labels_url":"https://api.github.com/repos/lomereiter/sambamba/issues/146/labels{/name}","comments_url":"https://api.github.com/repos/lomereiter/sambamba/issues/146/comments","events_url":"https://api.github.com/repos/lomereiter/sambamba/issues/146/events","html_url":"https://github.com/lomereiter/sambamba/issues/146","id":88995030,"number":146,"title":"Quality treshold in sambamba depth","user":{"login":"moonso","id":405278,"avatar_url":"https://avatars.githubusercontent.com/u/405278?v=3","gravatar_id":"","url":"https://api.github.com/users/moonso","html_url":"https://github.com/moonso","followers_url":"https://api.github.com/users/moonso/followers","following_url":"https://api.github.com/users/moonso/following{/other_user}","gists_url":"https://api.github.com/users/moonso/gists{/gist_id}","starred_url":"https://api.github.com/users/moonso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/moonso/subscriptions","organizations_url":"https://api.github.com/users/moonso/orgs","repos_url":"https://api.github.com/users/moonso/repos","events_url":"https://api.github.com/users/moonso/events{/privacy}","received_events_url":"https://api.github.com/users/moonso/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-06-17T11:51:25Z","updated_at":"2015-06-17T11:51:25Z","closed_at":null,"body":"I noticed that ```sambamba depth``` use only high quality reads when reporting coverage.\r\nIs there anyway to see the default value of this parameter.  \r\n\r\nWhen using ```--min-base-quality 0```  the same coverage is reported as I get without this flag, but with ```samtools tview``` I can see that there are multiple low quality reads that covers the positions of interest."}}