{"action":"created","issue":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/187","repository_url":"https://api.github.com/repos/gpertea/stringtie","labels_url":"https://api.github.com/repos/gpertea/stringtie/issues/187/labels{/name}","comments_url":"https://api.github.com/repos/gpertea/stringtie/issues/187/comments","events_url":"https://api.github.com/repos/gpertea/stringtie/issues/187/events","html_url":"https://github.com/gpertea/stringtie/issues/187","id":335982802,"node_id":"MDU6SXNzdWUzMzU5ODI4MDI=","number":187,"title":"Coverage inaccuracy from samtools","user":{"login":"jupiler55","id":30537885,"node_id":"MDQ6VXNlcjMwNTM3ODg1","avatar_url":"https://avatars2.githubusercontent.com/u/30537885?v=4","gravatar_id":"","url":"https://api.github.com/users/jupiler55","html_url":"https://github.com/jupiler55","followers_url":"https://api.github.com/users/jupiler55/followers","following_url":"https://api.github.com/users/jupiler55/following{/other_user}","gists_url":"https://api.github.com/users/jupiler55/gists{/gist_id}","starred_url":"https://api.github.com/users/jupiler55/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jupiler55/subscriptions","organizations_url":"https://api.github.com/users/jupiler55/orgs","repos_url":"https://api.github.com/users/jupiler55/repos","events_url":"https://api.github.com/users/jupiler55/events{/privacy}","received_events_url":"https://api.github.com/users/jupiler55/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-06-26T20:42:23Z","updated_at":"2018-06-26T21:10:22Z","closed_at":null,"author_association":"NONE","body":"The coverage reported by stringtie seems to be generated from \"samtools depth\", which by default only considers up to 8,000 reads at each position.  We have regions with much higher coverage and are thus getting inaccurate count.  StringTie doesn't seem to have an option to pass a parameter to \"samtools depth -d\", which sets the max coverage.  Requesting such option."},"comment":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/comments/400463451","html_url":"https://github.com/gpertea/stringtie/issues/187#issuecomment-400463451","issue_url":"https://api.github.com/repos/gpertea/stringtie/issues/187","id":400463451,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMDQ2MzQ1MQ==","user":{"login":"jupiler55","id":30537885,"node_id":"MDQ6VXNlcjMwNTM3ODg1","avatar_url":"https://avatars2.githubusercontent.com/u/30537885?v=4","gravatar_id":"","url":"https://api.github.com/users/jupiler55","html_url":"https://github.com/jupiler55","followers_url":"https://api.github.com/users/jupiler55/followers","following_url":"https://api.github.com/users/jupiler55/following{/other_user}","gists_url":"https://api.github.com/users/jupiler55/gists{/gist_id}","starred_url":"https://api.github.com/users/jupiler55/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jupiler55/subscriptions","organizations_url":"https://api.github.com/users/jupiler55/orgs","repos_url":"https://api.github.com/users/jupiler55/repos","events_url":"https://api.github.com/users/jupiler55/events{/privacy}","received_events_url":"https://api.github.com/users/jupiler55/received_events","type":"User","site_admin":false},"created_at":"2018-06-26T21:10:22Z","updated_at":"2018-06-26T21:10:22Z","author_association":"NONE","body":"it matches the numbers generated by samtools depth with default setting capped at 8k.    samtools depth -d 99999999 shows the actual coverage."}}
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