{"action":"created","issue":{"url":"https://api.github.com/repos/goblinhecker/SnIPRE-Input/issues/2","labels_url":"https://api.github.com/repos/goblinhecker/SnIPRE-Input/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/goblinhecker/SnIPRE-Input/issues/2/comments","events_url":"https://api.github.com/repos/goblinhecker/SnIPRE-Input/issues/2/events","html_url":"https://github.com/goblinhecker/SnIPRE-Input/issues/2","id":123618068,"number":2,"title":"How is the outgroup incoperated in the inputs for the snipre_prep?","user":{"login":"schnuffipc","id":16239600,"avatar_url":"https://avatars.githubusercontent.com/u/16239600?v=3","gravatar_id":"","url":"https://api.github.com/users/schnuffipc","html_url":"https://github.com/schnuffipc","followers_url":"https://api.github.com/users/schnuffipc/followers","following_url":"https://api.github.com/users/schnuffipc/following{/other_user}","gists_url":"https://api.github.com/users/schnuffipc/gists{/gist_id}","starred_url":"https://api.github.com/users/schnuffipc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schnuffipc/subscriptions","organizations_url":"https://api.github.com/users/schnuffipc/orgs","repos_url":"https://api.github.com/users/schnuffipc/repos","events_url":"https://api.github.com/users/schnuffipc/events{/privacy}","received_events_url":"https://api.github.com/users/schnuffipc/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-12-23T08:05:43Z","updated_at":"2016-01-01T20:00:58Z","closed_at":null,"body":"I couldn't find any reference to the outgroup other than 7) nout : outgroup x 2 (positive integer). \r\nSay I am using one outgroup, how is your program going to see it? Should it be as a .bam, should it be in the .vcf? \r\nThanks in advance"},"comment":{"url":"https://api.github.com/repos/goblinhecker/SnIPRE-Input/issues/comments/168334917","html_url":"https://github.com/goblinhecker/SnIPRE-Input/issues/2#issuecomment-168334917","issue_url":"https://api.github.com/repos/goblinhecker/SnIPRE-Input/issues/2","id":168334917,"user":{"login":"goblinhecker","id":12205238,"avatar_url":"https://avatars.githubusercontent.com/u/12205238?v=3","gravatar_id":"","url":"https://api.github.com/users/goblinhecker","html_url":"https://github.com/goblinhecker","followers_url":"https://api.github.com/users/goblinhecker/followers","following_url":"https://api.github.com/users/goblinhecker/following{/other_user}","gists_url":"https://api.github.com/users/goblinhecker/gists{/gist_id}","starred_url":"https://api.github.com/users/goblinhecker/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/goblinhecker/subscriptions","organizations_url":"https://api.github.com/users/goblinhecker/orgs","repos_url":"https://api.github.com/users/goblinhecker/repos","events_url":"https://api.github.com/users/goblinhecker/events{/privacy}","received_events_url":"https://api.github.com/users/goblinhecker/received_events","type":"User","site_admin":false},"created_at":"2016-01-01T20:00:58Z","updated_at":"2016-01-01T20:00:58Z","body":"Hello Eyan and Pnina,\r\n\r\nAs Eyal correctly figured out, my scripts WERE used with population data from species A mapped to reference genome of species B, and the VCF file reflected this. We had another VCF file for data from species B mapped to reference genome of species A. I am sorry that my documentation is not clear regarding this matter. \r\n\r\nIn my scripts, the outgroup (nout) and population size (npop) are just numbers, which I feed into the scripts written by Kirsten Eilertson (the actual SnIPRE program, available here: https://bustamantelab.stanford.edu/software). \r\n\r\nThank you,\r\nSunny."}}