{"action":"created","issue":{"url":"https://api.github.com/repos/morrislab/phylowgs/issues/21","labels_url":"https://api.github.com/repos/morrislab/phylowgs/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/morrislab/phylowgs/issues/21/comments","events_url":"https://api.github.com/repos/morrislab/phylowgs/issues/21/events","html_url":"https://github.com/morrislab/phylowgs/issues/21","id":117911131,"number":21,"title":"Question: How to run PhyloWGS jointly on multiple samples?","user":{"login":"armish","id":7809,"avatar_url":"https://avatars.githubusercontent.com/u/7809?v=3","gravatar_id":"","url":"https://api.github.com/users/armish","html_url":"https://github.com/armish","followers_url":"https://api.github.com/users/armish/followers","following_url":"https://api.github.com/users/armish/following{/other_user}","gists_url":"https://api.github.com/users/armish/gists{/gist_id}","starred_url":"https://api.github.com/users/armish/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/armish/subscriptions","organizations_url":"https://api.github.com/users/armish/orgs","repos_url":"https://api.github.com/users/armish/repos","events_url":"https://api.github.com/users/armish/events{/privacy}","received_events_url":"https://api.github.com/users/armish/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-11-19T21:25:10Z","updated_at":"2015-11-26T02:48:09Z","closed_at":null,"body":"Looks like the CLL example in the PhyloWGS paper was the result of a multi-sample run and you do explain the possibility of extending the method for multiple-sample analysis; but what exactly is needed for this? The SSM data doesn't encode for patient ID and your README file doesn't have any guidelines on how to evolve models in a multi-sample manner -- so I am a little bit lost on this one. Is there any documentation on this feature or on how to replicate the CLL analysis in your paper (so that I can use that as a see-by-example tutorial for myself)?\r\n\r\nThanks!\r\n-- Arman"},"comment":{"url":"https://api.github.com/repos/morrislab/phylowgs/issues/comments/159787759","html_url":"https://github.com/morrislab/phylowgs/issues/21#issuecomment-159787759","issue_url":"https://api.github.com/repos/morrislab/phylowgs/issues/21","id":159787759,"user":{"login":"armish","id":7809,"avatar_url":"https://avatars.githubusercontent.com/u/7809?v=3","gravatar_id":"","url":"https://api.github.com/users/armish","html_url":"https://github.com/armish","followers_url":"https://api.github.com/users/armish/followers","following_url":"https://api.github.com/users/armish/following{/other_user}","gists_url":"https://api.github.com/users/armish/gists{/gist_id}","starred_url":"https://api.github.com/users/armish/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/armish/subscriptions","organizations_url":"https://api.github.com/users/armish/orgs","repos_url":"https://api.github.com/users/armish/repos","events_url":"https://api.github.com/users/armish/events{/privacy}","received_events_url":"https://api.github.com/users/armish/received_events","type":"User","site_admin":false},"created_at":"2015-11-26T02:48:09Z","updated_at":"2015-11-26T02:48:09Z","body":"Thanks @AmitDeshwar! Does the order of the samples need to be same throughout the file and how do you encode the lack of a mutation in a particular sample?  "}}