{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/86","labels_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/86/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/86/comments","events_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/86/events","html_url":"https://github.com/arq5x/lumpy-sv/issues/86","id":82211104,"number":86,"title":"README is unclear about which bam files need to be sorted","user":{"login":"bjpop","id":214514,"avatar_url":"https://avatars.githubusercontent.com/u/214514?v=3","gravatar_id":"","url":"https://api.github.com/users/bjpop","html_url":"https://github.com/bjpop","followers_url":"https://api.github.com/users/bjpop/followers","following_url":"https://api.github.com/users/bjpop/following{/other_user}","gists_url":"https://api.github.com/users/bjpop/gists{/gist_id}","starred_url":"https://api.github.com/users/bjpop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bjpop/subscriptions","organizations_url":"https://api.github.com/users/bjpop/orgs","repos_url":"https://api.github.com/users/bjpop/repos","events_url":"https://api.github.com/users/bjpop/events{/privacy}","received_events_url":"https://api.github.com/users/bjpop/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-05-29T01:55:48Z","updated_at":"2015-06-01T12:49:50Z","closed_at":null,"body":"In the README it says \"All of the bam files that lumpy processes must be position sorted\".\r\n\r\nHowever, this does not appear to be true for the original sample.bam. Indeed, your example workflow does not sort the original sample.bam.\r\n\r\nCan you please clarify this detail in the README?"},"comment":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/comments/107429617","html_url":"https://github.com/arq5x/lumpy-sv/issues/86#issuecomment-107429617","issue_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/86","id":107429617,"user":{"login":"bjpop","id":214514,"avatar_url":"https://avatars.githubusercontent.com/u/214514?v=3","gravatar_id":"","url":"https://api.github.com/users/bjpop","html_url":"https://github.com/bjpop","followers_url":"https://api.github.com/users/bjpop/followers","following_url":"https://api.github.com/users/bjpop/following{/other_user}","gists_url":"https://api.github.com/users/bjpop/gists{/gist_id}","starred_url":"https://api.github.com/users/bjpop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bjpop/subscriptions","organizations_url":"https://api.github.com/users/bjpop/orgs","repos_url":"https://api.github.com/users/bjpop/repos","events_url":"https://api.github.com/users/bjpop/events{/privacy}","received_events_url":"https://api.github.com/users/bjpop/received_events","type":"User","site_admin":false},"created_at":"2015-06-01T12:49:49Z","updated_at":"2015-06-01T12:49:49Z","body":"Hi @ryanlayer,\r\n\r\nIn the example workflow, under \"Otherwise, data may be aligned with BWA-MEM\"\r\n\r\nThe examples shows how to use bwa-mem. It later shows how to use samtools to sort the splitter and the discordants. But it doesn't show a step that sorts the sample.bam. That would help when someone is following along the steps.\r\n\r\nI accidentally didn't sort the sample.bam, yet it still seemed to work."}}