{"action":"created","issue":{"url":"https://api.github.com/repos/mskcc/facets/issues/81","repository_url":"https://api.github.com/repos/mskcc/facets","labels_url":"https://api.github.com/repos/mskcc/facets/issues/81/labels{/name}","comments_url":"https://api.github.com/repos/mskcc/facets/issues/81/comments","events_url":"https://api.github.com/repos/mskcc/facets/issues/81/events","html_url":"https://github.com/mskcc/facets/issues/81","id":325536947,"node_id":"MDU6SXNzdWUzMjU1MzY5NDc=","number":81,"title":"About parameters setting for targeted panel","user":{"login":"BZ532","id":39542772,"node_id":"MDQ6VXNlcjM5NTQyNzcy","avatar_url":"https://avatars2.githubusercontent.com/u/39542772?v=4","gravatar_id":"","url":"https://api.github.com/users/BZ532","html_url":"https://github.com/BZ532","followers_url":"https://api.github.com/users/BZ532/followers","following_url":"https://api.github.com/users/BZ532/following{/other_user}","gists_url":"https://api.github.com/users/BZ532/gists{/gist_id}","starred_url":"https://api.github.com/users/BZ532/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BZ532/subscriptions","organizations_url":"https://api.github.com/users/BZ532/orgs","repos_url":"https://api.github.com/users/BZ532/repos","events_url":"https://api.github.com/users/BZ532/events{/privacy}","received_events_url":"https://api.github.com/users/BZ532/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-05-23T03:33:03Z","updated_at":"2018-06-08T10:08:47Z","closed_at":null,"author_association":"NONE","body":"Hi! \r\nWe've tried to use FACETS to call genome wide CNAs in a paired tumor-normal case, but we are not sure about  optimizing parameters like ndepth, snp.nbhd etc. to get reliable segmentation and CN calls.  In our case, the average sequencing depth of tumor and normal are 1000X and 100X respectively. The targeted panel  may cover ~800 het SNPs (heterozygosity rate: 0.25-0.75) .  In FACETS, is there any measurement to indicate users the reliability of the fitting? Or, can you recommend some parameter set for our trials,  or some guidelines to optimize parameters under which we could get reliable and stable calls? \r\nDefault parameters were used for SNP-pileup with pseudoSNP setting as 100. We've tried to increase ndepth, lower het.theshold and min.het , and change snp.nbhd in range of 100 to 250.  cncf file,  purity and ploidy fitting come differently under each combination. Except those \"unreliable\" flags, what should be considered to determine optimized parameters in our case ? Any suggestions will be helpful.  Thanks very much !!!\r\n"},"comment":{"url":"https://api.github.com/repos/mskcc/facets/issues/comments/395715863","html_url":"https://github.com/mskcc/facets/issues/81#issuecomment-395715863","issue_url":"https://api.github.com/repos/mskcc/facets/issues/81","id":395715863,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NTcxNTg2Mw==","user":{"login":"BZ532","id":39542772,"node_id":"MDQ6VXNlcjM5NTQyNzcy","avatar_url":"https://avatars2.githubusercontent.com/u/39542772?v=4","gravatar_id":"","url":"https://api.github.com/users/BZ532","html_url":"https://github.com/BZ532","followers_url":"https://api.github.com/users/BZ532/followers","following_url":"https://api.github.com/users/BZ532/following{/other_user}","gists_url":"https://api.github.com/users/BZ532/gists{/gist_id}","starred_url":"https://api.github.com/users/BZ532/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BZ532/subscriptions","organizations_url":"https://api.github.com/users/BZ532/orgs","repos_url":"https://api.github.com/users/BZ532/repos","events_url":"https://api.github.com/users/BZ532/events{/privacy}","received_events_url":"https://api.github.com/users/BZ532/received_events","type":"User","site_admin":false},"created_at":"2018-06-08T10:08:47Z","updated_at":"2018-06-08T10:08:47Z","author_association":"NONE","body":"Hi, veseshan:\r\n     Another problem about fit$seglen from emcncf fitting. I've noticed that not every sample has a numeric vector of fit$seglen. I am wondering why this happened. Could you please explain for such condition? Whether it may indicate a poor sample or something else? \r\nThank you!\r\n     "}}
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