{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1092","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1092/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1092/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1092/events","html_url":"https://github.com/broadinstitute/gatk/issues/1092","id":115560422,"number":1092,"title":"Profile SelectVariants against the GATK3 version","user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/profiling","name":"profiling","color":"bfd4f2"},{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/tools","name":"tools","color":"0052cc"}],"state":"open","locked":false,"assignee":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/broadinstitute/gatk/milestones/5","html_url":"https://github.com/broadinstitute/gatk/milestones/alpha","labels_url":"https://api.github.com/repos/broadinstitute/gatk/milestones/5/labels","id":1220227,"number":5,"title":"alpha","description":"","creator":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"open_issues":55,"closed_issues":114,"state":"open","created_at":"2015-07-22T13:37:37Z","updated_at":"2015-11-09T17:52:10Z","due_on":"2015-12-01T05:00:00Z","closed_at":null},"comments":4,"created_at":"2015-11-06T18:25:02Z","updated_at":"2015-11-09T19:00:56Z","closed_at":null,"body":"After https://github.com/broadinstitute/gatk/pull/792 is merged, ensure that our version of `SelectVariants` is as fast or faster than the GATK3 version on typical inputs."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/155156351","html_url":"https://github.com/broadinstitute/gatk/issues/1092#issuecomment-155156351","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1092","id":155156351,"user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"created_at":"2015-11-09T19:00:56Z","updated_at":"2015-11-09T19:00:56Z","body":"case1: local file CEUTrio.HiSeq.WGS.b37.bestPractices.b37.vcf 1.9G\r\ncommandline\r\n```\r\n-T SelectVariants -R /Users/akiezun/bin/reference/human_g1k_v37.fasta -V /Users/akiezun/bin/data/CEUTrio.HiSeq.WGS.b37.bestPractices.b37.vcf -select (vc.getGenotype(\"NA12878\").getPhredScaledQual() >= 90 && vc.getGenotype(\"NA12891\").getPhredScaledQual() >= 90 && vc.getGenotype(\"NA12892\").getPhredScaledQual() >= 90) && ((vc.getGenotype(\"NA12878\").isHomRef() && vc.getGenotype(\"NA12891\").isHomRef() && vc.getGenotype(\"NA12892\").isHomRef()) || (vc.getGenotype(\"NA12878\").isHomVar() && vc.getGenotype(\"NA12891\").isHomVar() && vc.getGenotype(\"NA12892\").isHomVar()) || (vc.getGenotype(\"NA12878\").isHet() && vc.getGenotype(\"NA12891\").isHomRef() && vc.getGenotype(\"NA12892\").isHomVar()) || (vc.getGenotype(\"NA12878\").isHet() && vc.getGenotype(\"NA12891\").isHomVar() && vc.getGenotype(\"NA12892\").isHomRef())) --out selectVariants_phasingFilterTest_gatk3.vcf\r\n```\r\n\r\n**1m56.863s** on GATK 3.4-46-gbc02625\r\n**1m24.934s** on GATK4.pre-alpha-100-g9200274\r\n\r\nrunning on Mac OS X 10.9.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_25-b17.\r\n\r\ntime gatk3 \r\n```\r\nreal\t1m56.863s\r\nuser\t1m58.199s\r\n```\r\n\r\ntime gatk4\r\n```\r\nreal\t1m24.934s\r\nuser\t1m33.709s\r\n```\r\n"}}