{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1214","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1214/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1214/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1214/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/pull/1214","id":131493520,"number":1214,"title":"Master","user":{"login":"apastore","id":6528310,"avatar_url":"https://avatars.githubusercontent.com/u/6528310?v=3","gravatar_id":"","url":"https://api.github.com/users/apastore","html_url":"https://github.com/apastore","followers_url":"https://api.github.com/users/apastore/followers","following_url":"https://api.github.com/users/apastore/following{/other_user}","gists_url":"https://api.github.com/users/apastore/gists{/gist_id}","starred_url":"https://api.github.com/users/apastore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apastore/subscriptions","organizations_url":"https://api.github.com/users/apastore/orgs","repos_url":"https://api.github.com/users/apastore/repos","events_url":"https://api.github.com/users/apastore/events{/privacy}","received_events_url":"https://api.github.com/users/apastore/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-02-04T22:33:37Z","updated_at":"2016-02-20T11:10:28Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls/1214","html_url":"https://github.com/chapmanb/bcbio-nextgen/pull/1214","diff_url":"https://github.com/chapmanb/bcbio-nextgen/pull/1214.diff","patch_url":"https://github.com/chapmanb/bcbio-nextgen/pull/1214.patch"},"body":"I am trying to Fix the MuTect2 vcf to match other paired sample caller\nand to support the gremline.py, but I have no idea how to deal with the\nout_file"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/186573912","html_url":"https://github.com/chapmanb/bcbio-nextgen/pull/1214#issuecomment-186573912","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1214","id":186573912,"user":{"login":"Eduardo-Alves","id":9776977,"avatar_url":"https://avatars.githubusercontent.com/u/9776977?v=3","gravatar_id":"","url":"https://api.github.com/users/Eduardo-Alves","html_url":"https://github.com/Eduardo-Alves","followers_url":"https://api.github.com/users/Eduardo-Alves/followers","following_url":"https://api.github.com/users/Eduardo-Alves/following{/other_user}","gists_url":"https://api.github.com/users/Eduardo-Alves/gists{/gist_id}","starred_url":"https://api.github.com/users/Eduardo-Alves/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Eduardo-Alves/subscriptions","organizations_url":"https://api.github.com/users/Eduardo-Alves/orgs","repos_url":"https://api.github.com/users/Eduardo-Alves/repos","events_url":"https://api.github.com/users/Eduardo-Alves/events{/privacy}","received_events_url":"https://api.github.com/users/Eduardo-Alves/received_events","type":"User","site_admin":false},"created_at":"2016-02-20T11:10:28Z","updated_at":"2016-02-20T11:10:28Z","body":"mutect2 doesnt have REJECT, SOMATIC filters in the vcf file and the anaysis is crashing at Germiline Extraction with an error:\r\nFile \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/germline.py\", line 109, in is_germline\r\nif \"SOMATIC\" in dict(rec.INFO):\r\nFile \"cyvcf2/cyvcf2.pyx\", line 1179, in cyvcf2.cyvcf2.INFO.__next_ (cyvcf2/cyvcf2.c:24884)\r\nFile \"cyvcf2/cyvcf2.pyx\", line 1126, in cyvcf2.cyvcf2.INFO._getval (cyvcf2/cyvcf2.c:23956)\r\nKeyError\r\n\r\nAccording to this post, all mutect2 output variants are somatic\r\n\r\nhttp://gatkforums.broadinstitute.org/gatk/discussion/6768/what-does-mutect-output-means\r\n\r\n\r\n(i also had to use mutect2 nightly because of a bug in mutect2 which doesn't handle -L parameter for tumor only. I am not sure if this bug affects all mutect2 results)\r\nhttp://gatkforums.broadinstitute.org/gatk/discussion/6690/mutect2-tumor-only-mode-empty-vcfs\r\n\r\nThank you\r\n\r\nEduardo\r\n\r\nexample mutect2 vcf output (now both indels and snps are reported)\r\n\r\n1 43815008 . TG T . clustered_events;homologous_mapping_event BaseQRankSum=-7.482;ClippingRankSum=0.401;DP=2026;ECNT=7;FS=3.007;HCNT=18;MAX_ED=80;MIN_ED=29;MQ=92.63;MQ0=0;MQRankSum=-6.091;NLOD=0.00;ReadPosRankSum=1.955;TLOD=38.77 GT:AD:AF 0/1:1989,30:0.015\r\n1 43815009 rs121913615 G T . clustered_events;homologous_mapping_event BaseQRankSum=12.469;ClippingRankSum=2.206;DB;DP=2026;ECNT=7;FS=2.581;HCNT=18;MAX_ED=80;MIN_ED=29;MQ=92.63;MQ0=0;MQRankSum=-18.528;NLOD=0.00;ReadPosRankSum=1.570;TLOD=374.92 GT:AD:AF:PGT:PID 0/1:1888,131:0.065:0|1:43815009_G_T"}}