{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1237","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1237/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1237/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1237/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1237","id":135202789,"number":1237,"title":"scalpel output vcf with inconsistent reference","user":{"login":"razZ0r","id":205865,"avatar_url":"https://avatars.githubusercontent.com/u/205865?v=3","gravatar_id":"","url":"https://api.github.com/users/razZ0r","html_url":"https://github.com/razZ0r","followers_url":"https://api.github.com/users/razZ0r/followers","following_url":"https://api.github.com/users/razZ0r/following{/other_user}","gists_url":"https://api.github.com/users/razZ0r/gists{/gist_id}","starred_url":"https://api.github.com/users/razZ0r/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/razZ0r/subscriptions","organizations_url":"https://api.github.com/users/razZ0r/orgs","repos_url":"https://api.github.com/users/razZ0r/repos","events_url":"https://api.github.com/users/razZ0r/events{/privacy}","received_events_url":"https://api.github.com/users/razZ0r/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-02-21T12:54:06Z","updated_at":"2016-02-22T22:26:42Z","closed_at":"2016-02-22T16:36:52Z","body":"GATK complains about an inconsistent reference in the scalpel output. Detailed error is [here](https://gist.github.com/razZ0r/3b25a35edb06c9caed83).\r\n\r\nThe problematic lines seem to be:\r\n\r\n>GL000225.1      206     .       CT      C       0.87    LowVafTumor;HighVafNormal;HighAltCntNormal;LowFisherScore;CHI2FILTER    ALTCOV=357;AVGCOV=7;BESTSTATE=11/11;CHI2=336.54;COVRATIO=0.02;COVSTATE=143,346/4,7/0,11;FISHERPHREDSCORE=0.87;INH=contamination;MINCOV=7;ZYG=het        GT:AD:DP        0/1:143,4:147   0/1:346,7:364\r\n>GL000225.1      206     .       GC      G       16.4    LowVafTumor;CHI2FILTER  ALTCOV=353;AVGCOV=11;BESTSTATE=21/01;CHI2=321.33;COVRATIO=0.03;COVSTATE=143,346/0,11/4,7;FISHERPHREDSCORE=16.4;INH=no;MINCOV=11;ZYG=het;SOMATIC GT:AD:DP        0/0:143,0:147   0/1:346,11:364\r\n\r\nAny ideas about the problem? Never used scalpel before.\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/187416795","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1237#issuecomment-187416795","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1237","id":187416795,"user":{"login":"razZ0r","id":205865,"avatar_url":"https://avatars.githubusercontent.com/u/205865?v=3","gravatar_id":"","url":"https://api.github.com/users/razZ0r","html_url":"https://github.com/razZ0r","followers_url":"https://api.github.com/users/razZ0r/followers","following_url":"https://api.github.com/users/razZ0r/following{/other_user}","gists_url":"https://api.github.com/users/razZ0r/gists{/gist_id}","starred_url":"https://api.github.com/users/razZ0r/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/razZ0r/subscriptions","organizations_url":"https://api.github.com/users/razZ0r/orgs","repos_url":"https://api.github.com/users/razZ0r/repos","events_url":"https://api.github.com/users/razZ0r/events{/privacy}","received_events_url":"https://api.github.com/users/razZ0r/received_events","type":"User","site_admin":false},"created_at":"2016-02-22T22:26:42Z","updated_at":"2016-02-22T22:26:42Z","body":"Thanks for the quick fix. I'll try to dig up a reproducible example, and will report back."}}