{"action":"created","issue":{"url":"https://api.github.com/repos/carolyncaron/GBSpipeline/issues/6","repository_url":"https://api.github.com/repos/carolyncaron/GBSpipeline","labels_url":"https://api.github.com/repos/carolyncaron/GBSpipeline/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/carolyncaron/GBSpipeline/issues/6/comments","events_url":"https://api.github.com/repos/carolyncaron/GBSpipeline/issues/6/events","html_url":"https://github.com/carolyncaron/GBSpipeline/issues/6","id":57653567,"number":6,"title":"Merge resulting .vcf files into a single file","user":{"login":"carolyncaron","id":7927760,"avatar_url":"https://avatars.githubusercontent.com/u/7927760?v=3","gravatar_id":"","url":"https://api.github.com/users/carolyncaron","html_url":"https://github.com/carolyncaron","followers_url":"https://api.github.com/users/carolyncaron/followers","following_url":"https://api.github.com/users/carolyncaron/following{/other_user}","gists_url":"https://api.github.com/users/carolyncaron/gists{/gist_id}","starred_url":"https://api.github.com/users/carolyncaron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/carolyncaron/subscriptions","organizations_url":"https://api.github.com/users/carolyncaron/orgs","repos_url":"https://api.github.com/users/carolyncaron/repos","events_url":"https://api.github.com/users/carolyncaron/events{/privacy}","received_events_url":"https://api.github.com/users/carolyncaron/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/carolyncaron/GBSpipeline/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-02-13T21:02:12Z","updated_at":"2016-03-28T21:55:41Z","closed_at":"2016-03-28T21:55:41Z","body":"Currently, each sample has a separate vcf file listing raw SNP calls. Since the natural next step is to merge them, have the pipeline do this automatically."},"comment":{"url":"https://api.github.com/repos/carolyncaron/GBSpipeline/issues/comments/202596102","html_url":"https://github.com/carolyncaron/GBSpipeline/issues/6#issuecomment-202596102","issue_url":"https://api.github.com/repos/carolyncaron/GBSpipeline/issues/6","id":202596102,"user":{"login":"carolyncaron","id":7927760,"avatar_url":"https://avatars.githubusercontent.com/u/7927760?v=3","gravatar_id":"","url":"https://api.github.com/users/carolyncaron","html_url":"https://github.com/carolyncaron","followers_url":"https://api.github.com/users/carolyncaron/followers","following_url":"https://api.github.com/users/carolyncaron/following{/other_user}","gists_url":"https://api.github.com/users/carolyncaron/gists{/gist_id}","starred_url":"https://api.github.com/users/carolyncaron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/carolyncaron/subscriptions","organizations_url":"https://api.github.com/users/carolyncaron/orgs","repos_url":"https://api.github.com/users/carolyncaron/repos","events_url":"https://api.github.com/users/carolyncaron/events{/privacy}","received_events_url":"https://api.github.com/users/carolyncaron/received_events","type":"User","site_admin":false},"created_at":"2016-03-28T21:55:41Z","updated_at":"2016-03-28T21:55:41Z","body":"The pipeline now has a single and multi-sample mode. Each sam file is BAMified, sorted and indexed as normal (although filtering for unaligned reads is done with the conversion to BAM and sorting of SAM files is removed, as it is no longer necessary) but the user can now specify through the config file whether to call mpileup and call SNPs on each sample individually (\"single\" mode), all at once (\"multi\" mode) or both (\"both\" mode)!"}}