{"action":"opened","issue":{"url":"https://api.github.com/repos/tonydisera/gene.iobio/issues/249","repository_url":"https://api.github.com/repos/tonydisera/gene.iobio","labels_url":"https://api.github.com/repos/tonydisera/gene.iobio/issues/249/labels{/name}","comments_url":"https://api.github.com/repos/tonydisera/gene.iobio/issues/249/comments","events_url":"https://api.github.com/repos/tonydisera/gene.iobio/issues/249/events","html_url":"https://github.com/tonydisera/gene.iobio/issues/249","id":140245273,"number":249,"title":"snpEff errors - ArrayIndexOutOfBounds","user":{"login":"tonydisera","id":8420103,"avatar_url":"https://avatars.githubusercontent.com/u/8420103?v=3","gravatar_id":"","url":"https://api.github.com/users/tonydisera","html_url":"https://github.com/tonydisera","followers_url":"https://api.github.com/users/tonydisera/followers","following_url":"https://api.github.com/users/tonydisera/following{/other_user}","gists_url":"https://api.github.com/users/tonydisera/gists{/gist_id}","starred_url":"https://api.github.com/users/tonydisera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tonydisera/subscriptions","organizations_url":"https://api.github.com/users/tonydisera/orgs","repos_url":"https://api.github.com/users/tonydisera/repos","events_url":"https://api.github.com/users/tonydisera/events{/privacy}","received_events_url":"https://api.github.com/users/tonydisera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-03-11T17:34:12Z","updated_at":"2016-03-11T17:34:12Z","closed_at":null,"body":"Select gene PDHA1 on spiked in platinum wgs variants for training session.  The following errors are produced in the snpEff error log:\r\n\r\nar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: Error while processing VCF entry (line 151) :\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: X        19369471        .        G        T        1039.74        PASS        AC=1;AF=0.001282;AN=780;BaseQRankSum=1.46;ClippingRankSum=0.391;DP=53498;FS=0.814;GQ_MEAN=109.63;GQ_STDDEV=53.79;InbreedingCoeff=-0.002;MLEAC=1;MLEAF=0.001282;MQ=60;MQ0=0;MQRankSum=0.303;NCC=0;QD=12.23;ReadPosRankSum=1.12;SOR=0.578;VQSLOD=2.15;culprit=FS;set=Intersection;VT_AC=1;VT_AN=4;BGAF_1KG=0;BGAF_EXAC=0        GT:AD:DP:GQ:PL        0/0:52,0:52:99:0,104,1642        0/1:44,41:85:99:1087,0,1161\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: java.lang.ArrayIndexOutOfBoundsException: 1\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: WARNINGS: Some warning were detected\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: Warning type        Number of warnings\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: WARNING_TRANSCRIPT_INCOMPLETE        1\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: WARNING_TRANSCRIPT_NO_START_CODON        1\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: java.lang.ArrayIndexOutOfBoundsException: 1\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: at ca.mcgill.mcb.pcingola.stats.TsTvStats.sample(TsTvStats.java:97)\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: at ca.mcgill.mcb.pcingola.stats.VcfStats.sample(VcfStats.java:57)\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateVcf(SnpEffCmdEff.java:301)\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:1026)\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: at edu.bostoncollege.chase.VariantMultiThread.run(VariantMultiThread.java:44)\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: Error while processing VCF entry (line 151) :\r\nMar 11 16:53:30 ip-172-32-45-253.ec2.internal docker[5307]: X        19369471        .        G        T        1039.74        PASS        "}}