{"action":"opened","issue":{"url":"https://api.github.com/repos/LynchLab/MAPGD/issues/7","labels_url":"https://api.github.com/repos/LynchLab/MAPGD/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/LynchLab/MAPGD/issues/7/comments","events_url":"https://api.github.com/repos/LynchLab/MAPGD/issues/7/events","html_url":"https://github.com/LynchLab/MAPGD/issues/7","id":100583029,"number":7,"title":"continuous pooled data from unknown number of individuals","user":{"login":"stsmall","id":2847551,"avatar_url":"https://avatars.githubusercontent.com/u/2847551?v=3","gravatar_id":"","url":"https://api.github.com/users/stsmall","html_url":"https://github.com/stsmall","followers_url":"https://api.github.com/users/stsmall/followers","following_url":"https://api.github.com/users/stsmall/following{/other_user}","gists_url":"https://api.github.com/users/stsmall/gists{/gist_id}","starred_url":"https://api.github.com/users/stsmall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stsmall/subscriptions","organizations_url":"https://api.github.com/users/stsmall/orgs","repos_url":"https://api.github.com/users/stsmall/repos","events_url":"https://api.github.com/users/stsmall/events{/privacy}","received_events_url":"https://api.github.com/users/stsmall/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-08-12T16:31:01Z","updated_at":"2015-08-12T16:31:01Z","closed_at":null,"body":"Dear Dr. Lynch,\r\nthank you for working on this code.\r\nI have 2 populations I would like to run a sliding window Fst analysis.\r\nThe 1st population is composed of 13 individual diploid genomes with SNPs called and filtered via freebayes. The 2nd population, and here is the crux of the issue, is a pooled population of an unknown number of genomes. Unknown because it is from a parasite infection with multiple parasites per blood sample. I have also used freebayes with the continuous-pool option to call and filter SNPs. \r\nFinally the questions:\r\n1) Can I use MAPGD on the continuous-pooled population or must I know the number of pooled individuals?\r\n2) Would it be better to run the cont-pooled.bam through mpileup, such that the .pro will contain rare alleles or just convert directly from vcf as I intend to do with the 13 individual diploid genomes?\r\n\r\nAlso as a note... this individual https://github.com/owensgl/reformat/blob/master/vcf2pro.pl wrote a script for converting vcf2pro which may be useful to users until you have a chance to supply your own.\r\n\r\nThank you,\r\nscott"}}