{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/4578","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4578/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4578/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4578/events","html_url":"https://github.com/broadinstitute/gatk/issues/4578","id":308617931,"number":4578,"title":"IndexOutOfBoundsException of Mutect2/GATK 4.0.2.1","user":{"login":"wangyugui","id":13562993,"avatar_url":"https://avatars2.githubusercontent.com/u/13562993?v=4","gravatar_id":"","url":"https://api.github.com/users/wangyugui","html_url":"https://github.com/wangyugui","followers_url":"https://api.github.com/users/wangyugui/followers","following_url":"https://api.github.com/users/wangyugui/following{/other_user}","gists_url":"https://api.github.com/users/wangyugui/gists{/gist_id}","starred_url":"https://api.github.com/users/wangyugui/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wangyugui/subscriptions","organizations_url":"https://api.github.com/users/wangyugui/orgs","repos_url":"https://api.github.com/users/wangyugui/repos","events_url":"https://api.github.com/users/wangyugui/events{/privacy}","received_events_url":"https://api.github.com/users/wangyugui/received_events","type":"User","site_admin":false},"labels":[{"id":620200639,"url":"https://api.github.com/repos/broadinstitute/gatk/labels/Mutect","name":"Mutect","color":"0052cc","default":false},{"id":153552584,"url":"https://api.github.com/repos/broadinstitute/gatk/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":{"login":"davidbenjamin","id":8438890,"avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false},"assignees":[{"login":"davidbenjamin","id":8438890,"avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/broadinstitute/gatk/milestones/17","html_url":"https://github.com/broadinstitute/gatk/milestone/17","labels_url":"https://api.github.com/repos/broadinstitute/gatk/milestones/17/labels","id":2574533,"number":17,"title":"Popularize Mutect 2 at the Broad","description":"We want others at the Broad, particularly the Genomics Platform and Cancer Genome Analysis group, to consider Mutect 2 (in GATK 4, of course) the only flavor of Mutect worth using.  To do this, we need to make it faster and we need additional validations.","creator":{"login":"davidbenjamin","id":8438890,"avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false},"open_issues":11,"closed_issues":75,"state":"open","created_at":"2017-06-09T19:53:45Z","updated_at":"2018-03-29T15:58:55Z","due_on":null,"closed_at":null},"comments":6,"created_at":"2018-03-26T15:20:22Z","updated_at":"2018-03-30T01:01:33Z","closed_at":null,"author_association":"NONE","body":"Hi.\r\n\r\nIndexOutOfBoundsException of Mutect2/GATK 4.0.2.1.\r\n\r\n```\r\n# java -jar /usr/hpc-bio/gatk/gatk-package-4.0.2.1-local.jar Mutect2 --verbosity WARNING -R /usr/bio-ref/GRCh38.p0.dnaref/dnaf.fa --germline-resource /usr/bio-ref/GRCh38.p0.dnaref/common.vcf --max-reads-per-alignment-start 100 -L X -I /biowrk/BaseSpace/bam.bwa/HiSe\r\nqX-PCR-free-v2.5-NA12878/md.bam -tumor HiSeqX-PCR-free-v2.5-NA12878 -O mutect2.tumor-only.vcf\r\n23:17:38.084 WARN  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM\r\n[March 26, 2018 11:17:38 PM CST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.08 minutes.\r\nRuntime.totalMemory()=2384986112\r\njava.lang.IndexOutOfBoundsException: Index: 0, Size: 0\r\n        at java.util.ArrayList.rangeCheck(ArrayList.java:657)\r\n        at java.util.ArrayList.get(ArrayList.java:433)\r\n        at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.isActive(Mutect2Engine.java:316)\r\n        at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:159)\r\n        at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135)\r\n        at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34)\r\n        at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:290)\r\n        at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:271)\r\n        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893)\r\n        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)\r\n        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)\r\n        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)\r\n        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:159)\r\n        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:202)\r\n        at org.broadinstitute.hellbender.Main.main(Main.java:288)\r\n```\r\n\r\nbut it works well on some other chr/region too."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/377416124","html_url":"https://github.com/broadinstitute/gatk/issues/4578#issuecomment-377416124","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4578","id":377416124,"user":{"login":"davidbenjamin","id":8438890,"avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false},"created_at":"2018-03-30T01:01:33Z","updated_at":"2018-03-30T01:01:33Z","author_association":"CONTRIBUTOR","body":"Ah, I see -- it seems like the difference is that the CAF includes the reference allele while AF doesn't.  Is that right?  So you would have `AF=0.1` and `CAF=0.9,0.1`.  I have to imagine there is some sort of bash trickery you could do.  For example, if every site has at least one alt allele, and therefore CAF always has a comma, you could delete everything from the `=` (exclusive) until the `,` (inclusive) like this (\r\n```bash\r\nsed sed 's/CAF\\=[^,]*\\,/AF\\=/g' dbsnp.vcf > dbsnp_for_m2.vcf\r\n```\r\nwhich replaces `CAF=[anything except a comma, which here is the ref AF],` with `AF=`."}}
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