{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1557","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1557/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1557/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1557/events","html_url":"https://github.com/broadinstitute/gatk/issues/1557","id":139021571,"number":1557,"title":"remove BAQ from BQSR (and validate results)","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},"labels":[{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/BestPracticesPipeline","name":"BestPracticesPipeline","color":"006b75"},{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/performance","name":"performance","color":"bfd4f2"}],"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/9","html_url":"https://github.com/broadinstitute/gatk/milestones/alpha-2","labels_url":"https://api.github.com/repos/broadinstitute/gatk/milestones/9/labels","id":1634880,"number":9,"title":"alpha-2","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":110,"closed_issues":19,"state":"open","created_at":"2016-03-09T17:39:39Z","updated_at":"2016-04-25T20:09:28Z","due_on":"2016-06-30T04:00:00Z","closed_at":null},"comments":13,"created_at":"2016-03-07T16:20:53Z","updated_at":"2016-04-26T22:35:59Z","closed_at":null,"body":"- [x] remove BAQ from code (provide a code path that skips BAQ)\r\n- [ ] run BaseRecalibrator skipping BAQ\r\n- [ ] run ApplyBQSR \r\n- [ ] compare base quals to a BAQ-full run\r\n- [ ] compare base quals after binning"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/214908294","html_url":"https://github.com/broadinstitute/gatk/issues/1557#issuecomment-214908294","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1557","id":214908294,"user":{"login":"yfarjoun","id":2745554,"avatar_url":"https://avatars.githubusercontent.com/u/2745554?v=3","gravatar_id":"","url":"https://api.github.com/users/yfarjoun","html_url":"https://github.com/yfarjoun","followers_url":"https://api.github.com/users/yfarjoun/followers","following_url":"https://api.github.com/users/yfarjoun/following{/other_user}","gists_url":"https://api.github.com/users/yfarjoun/gists{/gist_id}","starred_url":"https://api.github.com/users/yfarjoun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yfarjoun/subscriptions","organizations_url":"https://api.github.com/users/yfarjoun/orgs","repos_url":"https://api.github.com/users/yfarjoun/repos","events_url":"https://api.github.com/users/yfarjoun/events{/privacy}","received_events_url":"https://api.github.com/users/yfarjoun/received_events","type":"User","site_admin":false},"created_at":"2016-04-26T22:35:59Z","updated_at":"2016-04-26T22:35:59Z","body":"yeah, this isn't miniscule...\n\nOn Tue, Apr 26, 2016 at 3:54 PM, Adam Kiezun <notifications@github.com>\nwrote:\n\n> Update on a 30GB exome file.\n>\n> So, 11% of bases change quals by 11 or more (negative sign here means that\n> quals \"improved\" when baq was off). Binned results follow, unbinned at the\n> end\n>\n> binned summary\n> diff    count   percent\n> -20 1505928      0.00753545014704519\n> -10 2294198573  11.4798443048165\n> -4  3            1.5011574551463e-08\n> 0   17621174464 88.173858050224\n> 1   16304311     0.0815844600289127\n> 2   753960       0.00377270891627368\n> 3   22026        0.000110214980356841\n> 4   1710832      0.00856076070434285\n> 10  48909067     0.244734035171\n>\n> binned (R1 and R2 are reads with and without BAQ, respectively)\n> R1     R2    diff       count           percent\n> 1       1       0       11046302       0.0552741286636583\n> 2       1       1       134293         0.000671983127079873\n> 2       2       0       5439108879    27.2165294768776\n> 3       1       2       273            1.36605328418313e-06\n> 3       2       1       1650911        0.00826092451811011\n> 3       3       0       5257473        0.0263076492972679\n> 4       1       3       4151           2.0771015321041e-05\n> 4       2       2       30057          0.000150400965431108\n> 4       3       1       1721174        0.00861251060567992\n> 4       4       0       14421926       0.0721652724415608\n> 5       2       3       7355           3.68033769420034e-05\n> 5       3       2       195142         0.000976462893707197\n> 5       4       1       6194067        0.0309942328490856\n> 5       5       0       7202415        0.0360398632410251\n> 6       3       3       10520          5.26405880937969e-05\n> 6       4       2       528488         0.00264447900385119\n> 6       5       1       6603866        0.0330448089289572\n> 6       6       0       12574438       0.0629207044932497\n> 6       10      -4      3              1.5011574551463e-08\n> 10      6       4       1710832        0.00856076070434285\n> 10      10      0       97036068       0.485554722987611\n> 20      10      10      1339792        0.0067041291638179\n> 20      20      0       490579807      2.45479178207428\n> 20      30      -10     1160138        0.00580516602566172\n> 20      40      -20     1505928        0.00753545014704519\n> 30      20      10      22329747       0.111734887268602\n> 30      30      0       2943018882     14.7264491178354\n> 30      40      -10     2293038435     11.4740391387908\n> 40      30      10      25239528       0.126295018738579\n> 40      40      0       8600928274     43.0378253323123\n>\n> unbinned summary (negative numbers mean removing BAQ \"improved\" base quals)\n> diff    count\n> -15     386396\n> -14     1625384\n> -13     1550996\n> -12     4846154\n> -11     7714911\n> -10     11818590\n> -9      39209516\n> -8      66850047\n> -7      127996955\n> -6      299319054\n> -5      559321479\n> -4      981648925\n> -3      1706215870\n> -2      2799767852\n> -1      3603802916\n> 0       9088821157\n> 1       628927858\n> 2       43909936\n> 3       7743783\n> 4       2677478\n> 5       312790\n> 6       111117\n>\n> (skipping unbinned full results - too big to be useful here)\n>\n> @eitanbanks <https://github.com/eitanbanks> @yfarjoun\n> <https://github.com/yfarjoun> WDYT? running HC seems reasonable given 10%\n> of bases changed by Q10 or more.\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly or view it on GitHub\n> <https://github.com/broadinstitute/gatk/issues/1557#issuecomment-214866819>\n>\n"}}