{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/41","labels_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/41/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/41/comments","events_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/41/events","html_url":"https://github.com/arq5x/lumpy-sv/issues/41","id":45017893,"number":41,"title":"lumpy-sv: both paired and split reads. Issue with bam file with split-reads.","user":{"login":"dashainparis","id":3019242,"avatar_url":"https://avatars.githubusercontent.com/u/3019242?v=3","gravatar_id":"","url":"https://api.github.com/users/dashainparis","html_url":"https://github.com/dashainparis","followers_url":"https://api.github.com/users/dashainparis/followers","following_url":"https://api.github.com/users/dashainparis/following{/other_user}","gists_url":"https://api.github.com/users/dashainparis/gists{/gist_id}","starred_url":"https://api.github.com/users/dashainparis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dashainparis/subscriptions","organizations_url":"https://api.github.com/users/dashainparis/orgs","repos_url":"https://api.github.com/users/dashainparis/repos","events_url":"https://api.github.com/users/dashainparis/events{/privacy}","received_events_url":"https://api.github.com/users/dashainparis/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":11,"created_at":"2014-10-06T18:28:30Z","updated_at":"2015-07-21T19:31:16Z","closed_at":"2014-10-09T12:42:45Z","body":"Hello, I've tried your tool for both paired and split reads. I took all the steps with extracting split-read, re-alignment and sorting reads with your scripts and it worked perfectly fine. But on the last step which corresponds directly to the lumpy I had the following error:\r\n\r\nCould not open input BAM files: BamMultiReader::Open: unable to open inconsistent files: \t\r\nBamMultiReader::ValidateReaders: mismatched sort order in /Users/dasha/PhD/lumpy-sv/data/sim_soft.sort.bam, expected , but found coordinate.\r\n\r\nIs that mean that the file was not sorted correct? I viewed the sim_soft.sort.bam in sam format and checked and it is seems to be sorted. To sort the file I used the commend that you recommend:\r\n\r\n./samtools sort ~/PhD/lumpy-sv/data/sim_soft.bam sim_soft.sort\r\n\r\nDo you have any recommendations?\r\n\r\nThank you in advance!\r\n\r\nDaria"},"comment":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/comments/123455151","html_url":"https://github.com/arq5x/lumpy-sv/issues/41#issuecomment-123455151","issue_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/41","id":123455151,"user":{"login":"ryanlayer","id":607057,"avatar_url":"https://avatars.githubusercontent.com/u/607057?v=3","gravatar_id":"","url":"https://api.github.com/users/ryanlayer","html_url":"https://github.com/ryanlayer","followers_url":"https://api.github.com/users/ryanlayer/followers","following_url":"https://api.github.com/users/ryanlayer/following{/other_user}","gists_url":"https://api.github.com/users/ryanlayer/gists{/gist_id}","starred_url":"https://api.github.com/users/ryanlayer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ryanlayer/subscriptions","organizations_url":"https://api.github.com/users/ryanlayer/orgs","repos_url":"https://api.github.com/users/ryanlayer/repos","events_url":"https://api.github.com/users/ryanlayer/events{/privacy}","received_events_url":"https://api.github.com/users/ryanlayer/received_events","type":"User","site_admin":false},"created_at":"2015-07-21T19:31:16Z","updated_at":"2015-07-21T19:31:16Z","body":"Can you check the headers of your BAM files?  Do they all state coordinate\nsorted?\n\nOn Tue, Jul 14, 2015 at 10:54 AM, donthu <notifications@github.com> wrote:\n\n> When I ran with discordants bam I did not get the error. My discordants\n> bam was sorted.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/arq5x/lumpy-sv/issues/41#issuecomment-121269535>.\n>\n\n\n\n-- \nRyan Layer\n"}}