{"action":"created","issue":{"url":"https://api.github.com/repos/cc2qe/svtyper/issues/7","labels_url":"https://api.github.com/repos/cc2qe/svtyper/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/cc2qe/svtyper/issues/7/comments","events_url":"https://api.github.com/repos/cc2qe/svtyper/issues/7/events","html_url":"https://github.com/cc2qe/svtyper/issues/7","id":70330401,"number":7,"title":"ValueError: mate not found","user":{"login":"MinocheAE","id":11867037,"avatar_url":"https://avatars.githubusercontent.com/u/11867037?v=3","gravatar_id":"","url":"https://api.github.com/users/MinocheAE","html_url":"https://github.com/MinocheAE","followers_url":"https://api.github.com/users/MinocheAE/followers","following_url":"https://api.github.com/users/MinocheAE/following{/other_user}","gists_url":"https://api.github.com/users/MinocheAE/gists{/gist_id}","starred_url":"https://api.github.com/users/MinocheAE/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MinocheAE/subscriptions","organizations_url":"https://api.github.com/users/MinocheAE/orgs","repos_url":"https://api.github.com/users/MinocheAE/repos","events_url":"https://api.github.com/users/MinocheAE/events{/privacy}","received_events_url":"https://api.github.com/users/MinocheAE/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-04-23T07:05:27Z","updated_at":"2015-04-23T11:45:14Z","closed_at":null,"body":"Hi, sounds like a interesting tool. Is there a detailed description what it actually does? Does it compare the coverage within and outside of the event? How many flanking bases are considered? \r\n\r\nThis is the error message I get:\r\n  File \"pysam/calignmentfile.pyx\", line 836, in pysam.calignmentfile.AlignmentFile.mate (pysam/calignmentfile.c:10945)\r\nValueError: mate not found\r\n\r\nI used BWA MEM for the alignment, called multiple samples with lumpy-sv. From looking at the svtyper script, it seems that it does support multiple samples, if bams are provided in a comma seperated list. If I split the multivcf per sample and run svtyper in the single sample mode or if svtyper in the multisample mode the error message stays the same.\r\n\r\nDo you have any idea what went wrong?\r\n\r\nSome lines actually got processed. The last output line is:\r\n1       823747  12      N       <DEL>   733.59  .       SVTYPE=DEL;SVLEN=-206;END=823953;STRANDS=+-:2;IMPRECISE;CIPOS=-7,8;CIEND=-1,9;CIPOS95=-2,4;CIEND95=0,9;SU=2;PE=0;SR=2   GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO   0/1:0:0:0:200:733.59:-83,-9,-106:333:252:81     ./.:0:0:0:.:.:.:.:.:.   ./.:0:0:0:.:.:.:.:.:.   ./.:0:0:0:.:.:.:.:.:.   ./.:2:0:2:.:.:.:.:.:.\r\n\r\nStrange that only sample got genotyped. The corresponding lines in the input file:\r\n1       823747  12      N       <DEL>   .       .       SVTYPE=DEL;STRANDS=+-:2;SVLEN=-206;END=823953;CIPOS=-7,8;CIEND=-1,9;CIPOS95=-2,4;CIEND95=0,9;IMPRECISE;SU=2;PE=0;SR=2   GT:SU:PE:SR     ./.:0:0:0       ./.:0:0:0       ./.:0:0:0       ./.:0:0:0       ./.:2:0:2\r\n1       829170  13      N       <DEL>   .       .       SVTYPE=DEL;STRANDS=+-:9;SVLEN=-35;END=829205;CIPOS=-9,8;CIEND=-5,3;CIPOS95=0,0;CIEND95=0,0;SU=9;PE=1;SR=8       GT:SU:PE:SR     ./.:4:0:4       ./.:2:0:2       ./.:1:1:0       ./.:2:0:2       ./.:0:0:0\r\n\r\nThanks\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/cc2qe/svtyper/issues/comments/95558085","html_url":"https://github.com/cc2qe/svtyper/issues/7#issuecomment-95558085","issue_url":"https://api.github.com/repos/cc2qe/svtyper/issues/7","id":95558085,"user":{"login":"cc2qe","id":3903682,"avatar_url":"https://avatars.githubusercontent.com/u/3903682?v=3","gravatar_id":"","url":"https://api.github.com/users/cc2qe","html_url":"https://github.com/cc2qe","followers_url":"https://api.github.com/users/cc2qe/followers","following_url":"https://api.github.com/users/cc2qe/following{/other_user}","gists_url":"https://api.github.com/users/cc2qe/gists{/gist_id}","starred_url":"https://api.github.com/users/cc2qe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cc2qe/subscriptions","organizations_url":"https://api.github.com/users/cc2qe/orgs","repos_url":"https://api.github.com/users/cc2qe/repos","events_url":"https://api.github.com/users/cc2qe/events{/privacy}","received_events_url":"https://api.github.com/users/cc2qe/received_events","type":"User","site_admin":false},"created_at":"2015-04-23T11:45:14Z","updated_at":"2015-04-23T11:45:14Z","body":"SVTyper compares the number of non-reference to reference reads at each breakpoint. A detailed description is in the Methods section of the SpeedSeq pre-print: http://biorxiv.org/content/early/2014/12/05/012179\r\n\r\nThe flank distance is a command line variable, but it's 20 by default.\r\n\r\nThe error you're seeing is because SVTyper cannot find the mate of a paired-end read. Is is possible that some mates are missing from your BAM file? Or are there single-end reads in it?\r\n\r\nIn general, SVTyper will be much faster if mate tags (MC, MQ) are present in your BAM, since without them it must seek to the corresponding mate position in the BAM. You may want to consider running SAMBLASTER with --addMateTags on your BAMs.\r\n\r\nI also just pushed some of the recent dev branch changes to the master branch, so you might try downloading the updated version. But I doubt that it will affect the error you're seeing."}}