{"action":"created","issue":{"url":"https://api.github.com/repos/pcingola/SnpEff/issues/96","labels_url":"https://api.github.com/repos/pcingola/SnpEff/issues/96/labels{/name}","comments_url":"https://api.github.com/repos/pcingola/SnpEff/issues/96/comments","events_url":"https://api.github.com/repos/pcingola/SnpEff/issues/96/events","html_url":"https://github.com/pcingola/SnpEff/issues/96","id":109615793,"number":96,"title":"Hgvs transcript NullPointerException for structural variants","user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=3","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-10-03T10:12:13Z","updated_at":"2015-10-03T13:37:05Z","closed_at":null,"body":"Pablo;\r\nWe've been working to add support for annotating structural variants with snpEff (4.1k) and ran into NullPointerExceptions when calculating HgvsProtein transcripts:\r\n```\r\njava.lang.NullPointerException\r\n        at ca.mcgill.mcb.pcingola.interval.Transcript.apply(Transcript.java:327)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.HgvsProtein.posFs(HgvsProtein.java:322)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.HgvsProtein.toString(HgvsProtein.java:473)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.VariantEffect.getHgvsProt(VariantEffect.java:540)\r\n        at ca.mcgill.mcb.pcingola.vcf.VcfEffect.set(VcfEffect.java:1028)\r\n        at ca.mcgill.mcb.pcingola.vcf.VcfEffect.<init>(VcfEffect.java:145)\r\n        at ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.addInfo(VcfOutputFormatter.java:97)\r\n        at ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.toString(VcfOutputFormatter.java:285)\r\n        at ca.mcgill.mcb.pcingola.outputFormatter.OutputFormatter.endSection(OutputFormatter.java:112)\r\n        at ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.endSection(VcfOutputFormatter.java:229)\r\n        at ca.mcgill.mcb.pcingola.outputFormatter.OutputFormatter.printSection(OutputFormatter.java:145)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:276)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:443)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:969)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:921)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:905)\r\n        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:128)\r\n```\r\nThis seems general and I could reproduce with output from 4 different callers (CNVkit, Lumpy, WHAM and Manta) and both human build 37 and 38. Here are two example files with the problems (https://gist.github.com/chapmanb/de12e55bbdefd5ea5824) that you can reproduce with:\r\n```\r\nsnpEff -Xms750m -Xmx6g -dataDir $datadir GRCh37.75 hgvs-error-37.vcf > hgvs-error-37-snpeff.vcf\r\nsnpEff -Xms750m -Xmx6g -dataDir $datadir GRCh38.78 hgvs-error-38.vcf > hgvs-error-38-snpeff.vcf\r\n```\r\nRight now it looks like you call this HGVS prep code by default, but It would be fine to not have HGVS output for structural variants (via `-noHgvs` or other options). Thanks so much for any help or suggestions. "},"comment":{"url":"https://api.github.com/repos/pcingola/SnpEff/issues/comments/145249490","html_url":"https://github.com/pcingola/SnpEff/issues/96#issuecomment-145249490","issue_url":"https://api.github.com/repos/pcingola/SnpEff/issues/96","id":145249490,"user":{"login":"pcingola","id":1334427,"avatar_url":"https://avatars.githubusercontent.com/u/1334427?v=3","gravatar_id":"","url":"https://api.github.com/users/pcingola","html_url":"https://github.com/pcingola","followers_url":"https://api.github.com/users/pcingola/followers","following_url":"https://api.github.com/users/pcingola/following{/other_user}","gists_url":"https://api.github.com/users/pcingola/gists{/gist_id}","starred_url":"https://api.github.com/users/pcingola/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pcingola/subscriptions","organizations_url":"https://api.github.com/users/pcingola/orgs","repos_url":"https://api.github.com/users/pcingola/repos","events_url":"https://api.github.com/users/pcingola/events{/privacy}","received_events_url":"https://api.github.com/users/pcingola/received_events","type":"User","site_admin":false},"created_at":"2015-10-03T13:37:05Z","updated_at":"2015-10-03T13:37:05Z","body":"\r\nCan you send a sample input VCF file that produces this error and the command line you are using?\r\n\r\n"}}