{"action":"created","issue":{"url":"https://api.github.com/repos/mskcc/facets/issues/26","repository_url":"https://api.github.com/repos/mskcc/facets","labels_url":"https://api.github.com/repos/mskcc/facets/issues/26/labels{/name}","comments_url":"https://api.github.com/repos/mskcc/facets/issues/26/comments","events_url":"https://api.github.com/repos/mskcc/facets/issues/26/events","html_url":"https://github.com/mskcc/facets/issues/26","id":194470072,"number":26,"title":"mouse \"chr20 zero snps\" error","user":{"login":"lordzappo","id":1440762,"avatar_url":"https://avatars.githubusercontent.com/u/1440762?v=3","gravatar_id":"","url":"https://api.github.com/users/lordzappo","html_url":"https://github.com/lordzappo","followers_url":"https://api.github.com/users/lordzappo/followers","following_url":"https://api.github.com/users/lordzappo/following{/other_user}","gists_url":"https://api.github.com/users/lordzappo/gists{/gist_id}","starred_url":"https://api.github.com/users/lordzappo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lordzappo/subscriptions","organizations_url":"https://api.github.com/users/lordzappo/orgs","repos_url":"https://api.github.com/users/lordzappo/repos","events_url":"https://api.github.com/users/lordzappo/events{/privacy}","received_events_url":"https://api.github.com/users/lordzappo/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":12,"created_at":"2016-12-08T23:13:23Z","updated_at":"2016-12-09T18:30:56Z","closed_at":"2016-12-09T16:33:33Z","body":"Loading required package: pctGCdata\r\nError in segsnps(dmat, cval, hetscale) : chr20 has ZERO snps\r\nCalls: facets_iteration -> preProcSample -> segsnps\r\nExecution halted\r\n\r\n\r\nMouse has 1-19, X,Y, so should the segsnps method be altered slightly?  My counts file certainly has 1-19, X, and Y.  \r\n\r\n@soccin- have you run into this before?\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/mskcc/facets/issues/comments/266086419","html_url":"https://github.com/mskcc/facets/issues/26#issuecomment-266086419","issue_url":"https://api.github.com/repos/mskcc/facets/issues/26","id":266086419,"user":{"login":"veseshan","id":12280668,"avatar_url":"https://avatars.githubusercontent.com/u/12280668?v=3","gravatar_id":"","url":"https://api.github.com/users/veseshan","html_url":"https://github.com/veseshan","followers_url":"https://api.github.com/users/veseshan/followers","following_url":"https://api.github.com/users/veseshan/following{/other_user}","gists_url":"https://api.github.com/users/veseshan/gists{/gist_id}","starred_url":"https://api.github.com/users/veseshan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/veseshan/subscriptions","organizations_url":"https://api.github.com/users/veseshan/orgs","repos_url":"https://api.github.com/users/veseshan/repos","events_url":"https://api.github.com/users/veseshan/events{/privacy}","received_events_url":"https://api.github.com/users/veseshan/received_events","type":"User","site_admin":false},"created_at":"2016-12-09T18:30:56Z","updated_at":"2016-12-09T18:30:56Z","body":"Then FACETS will probably give the wrong answers all the time. We should think about restricting FACETS to cases with sufficient het SNPs (at at least 5% of snps should be hets) and do a pure total copy number package for these cases and low-pass WGS."}}
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