{"action":"created","issue":{"url":"https://api.github.com/repos/morrislab/phylowgs/issues/71","repository_url":"https://api.github.com/repos/morrislab/phylowgs","labels_url":"https://api.github.com/repos/morrislab/phylowgs/issues/71/labels{/name}","comments_url":"https://api.github.com/repos/morrislab/phylowgs/issues/71/comments","events_url":"https://api.github.com/repos/morrislab/phylowgs/issues/71/events","html_url":"https://github.com/morrislab/phylowgs/issues/71","id":286621515,"number":71,"title":"How to handle \"cellular_prevalence\" in cnvs.txt if missing data","user":{"login":"ozill12","id":2716470,"avatar_url":"https://avatars0.githubusercontent.com/u/2716470?v=4","gravatar_id":"","url":"https://api.github.com/users/ozill12","html_url":"https://github.com/ozill12","followers_url":"https://api.github.com/users/ozill12/followers","following_url":"https://api.github.com/users/ozill12/following{/other_user}","gists_url":"https://api.github.com/users/ozill12/gists{/gist_id}","starred_url":"https://api.github.com/users/ozill12/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ozill12/subscriptions","organizations_url":"https://api.github.com/users/ozill12/orgs","repos_url":"https://api.github.com/users/ozill12/repos","events_url":"https://api.github.com/users/ozill12/events{/privacy}","received_events_url":"https://api.github.com/users/ozill12/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-01-08T01:57:47Z","updated_at":"2018-02-06T19:52:57Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\nI am trying to run phyloWGS with both ssm and cnv data, but the copy number tool I am using (sequenza) does not provide estimates of clonal fraction/cellular prevalence per segment.  Would it be appropriate the use the estimated cellularity (fraction of tumor cells in the sample) value as a constant/dummy value in this column of cnvs.txt when running the parser, or what do you recommend doing when cellular prevalence per segment is missing?\r\nThanks,\r\nOliver"},"comment":{"url":"https://api.github.com/repos/morrislab/phylowgs/issues/comments/363544482","html_url":"https://github.com/morrislab/phylowgs/issues/71#issuecomment-363544482","issue_url":"https://api.github.com/repos/morrislab/phylowgs/issues/71","id":363544482,"user":{"login":"jwintersinger","id":266021,"avatar_url":"https://avatars0.githubusercontent.com/u/266021?v=4","gravatar_id":"","url":"https://api.github.com/users/jwintersinger","html_url":"https://github.com/jwintersinger","followers_url":"https://api.github.com/users/jwintersinger/followers","following_url":"https://api.github.com/users/jwintersinger/following{/other_user}","gists_url":"https://api.github.com/users/jwintersinger/gists{/gist_id}","starred_url":"https://api.github.com/users/jwintersinger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jwintersinger/subscriptions","organizations_url":"https://api.github.com/users/jwintersinger/orgs","repos_url":"https://api.github.com/users/jwintersinger/repos","events_url":"https://api.github.com/users/jwintersinger/events{/privacy}","received_events_url":"https://api.github.com/users/jwintersinger/received_events","type":"User","site_admin":false},"created_at":"2018-02-06T19:52:57Z","updated_at":"2018-02-06T19:52:57Z","author_association":"CONTRIBUTOR","body":"Hi @ozill12,\r\n\r\nSequenza doesn't seem to do subclonal copy number calling, so just providing the cellularity estimated by Sequenza should be okay. We won't be able to correct for subclonal copy-number changes' effects on mutation frequency, but that's still better than running without copy-number calls.\r\n\r\nPlease let us know if we can help with anything else!"}}
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