{"action":"created","issue":{"url":"https://api.github.com/repos/parklab/Software-Issues/issues/17","repository_url":"https://api.github.com/repos/parklab/Software-Issues","labels_url":"https://api.github.com/repos/parklab/Software-Issues/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/parklab/Software-Issues/issues/17/comments","events_url":"https://api.github.com/repos/parklab/Software-Issues/issues/17/events","html_url":"https://github.com/parklab/Software-Issues/issues/17","id":344882604,"node_id":"MDU6SXNzdWUzNDQ4ODI2MDQ=","number":17,"title":"Noisy CNV profile with many focal events","user":{"login":"scottx611x","id":5629547,"node_id":"MDQ6VXNlcjU2Mjk1NDc=","avatar_url":"https://avatars2.githubusercontent.com/u/5629547?v=4","gravatar_id":"","url":"https://api.github.com/users/scottx611x","html_url":"https://github.com/scottx611x","followers_url":"https://api.github.com/users/scottx611x/followers","following_url":"https://api.github.com/users/scottx611x/following{/other_user}","gists_url":"https://api.github.com/users/scottx611x/gists{/gist_id}","starred_url":"https://api.github.com/users/scottx611x/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/scottx611x/subscriptions","organizations_url":"https://api.github.com/users/scottx611x/orgs","repos_url":"https://api.github.com/users/scottx611x/repos","events_url":"https://api.github.com/users/scottx611x/events{/privacy}","received_events_url":"https://api.github.com/users/scottx611x/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-07-26T15:01:34Z","updated_at":"2018-07-26T15:02:40Z","closed_at":null,"author_association":"MEMBER","body":"Submitter: Rashesh Sanghvi\r\nEmail: rsanghvi@nygenome.org\r\nHello,\r\nI am currently benchmarking bicseq2 version 0.2.4 for incorporating in our pipeline. We have been using nbicseq v0.7a in our pipeline. \r\nWhile testing I ran multiple iterations of bicseq2 on the same samples, to determine the reproducibility of the CNV calls. I noticed that probably 1 out of 10 iterations had noisy focal events being called. \r\nI increased the subsampling fraction of the reads to 0.001. I saw the same issue. These samples have a single read length(151 bp). Coverage is 50X normal 90X tumor. \r\nI am attaching the CNV plots for the same.\r\n\r\n1) Have you seen this issue before? If yes then, what would you suggest as the solution? \r\n2) Is there a way to increase the reproducibility from iteration to iteration?\r\n\r\nYour support and suggestions are appreciated. \r\n\r\nThank you,\r\nRashesh"},"comment":{"url":"https://api.github.com/repos/parklab/Software-Issues/issues/comments/408127861","html_url":"https://github.com/parklab/Software-Issues/issues/17#issuecomment-408127861","issue_url":"https://api.github.com/repos/parklab/Software-Issues/issues/17","id":408127861,"node_id":"MDEyOklzc3VlQ29tbWVudDQwODEyNzg2MQ==","user":{"login":"Rashesh7","id":4691098,"node_id":"MDQ6VXNlcjQ2OTEwOTg=","avatar_url":"https://avatars2.githubusercontent.com/u/4691098?v=4","gravatar_id":"","url":"https://api.github.com/users/Rashesh7","html_url":"https://github.com/Rashesh7","followers_url":"https://api.github.com/users/Rashesh7/followers","following_url":"https://api.github.com/users/Rashesh7/following{/other_user}","gists_url":"https://api.github.com/users/Rashesh7/gists{/gist_id}","starred_url":"https://api.github.com/users/Rashesh7/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Rashesh7/subscriptions","organizations_url":"https://api.github.com/users/Rashesh7/orgs","repos_url":"https://api.github.com/users/Rashesh7/repos","events_url":"https://api.github.com/users/Rashesh7/events{/privacy}","received_events_url":"https://api.github.com/users/Rashesh7/received_events","type":"User","site_admin":false},"created_at":"2018-07-26T15:02:40Z","updated_at":"2018-07-26T15:02:40Z","author_association":"NONE","body":"This is a duplicate issue. I already submitted it on github issues. Sorry about that. "}}
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