{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1502","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1502/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1502/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1502/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1502","id":169675586,"number":1502,"title":"RNA-seq variant calling: precision might be improved","user":{"login":"naumenko-sa","id":13981803,"avatar_url":"https://avatars.githubusercontent.com/u/13981803?v=3","gravatar_id":"","url":"https://api.github.com/users/naumenko-sa","html_url":"https://github.com/naumenko-sa","followers_url":"https://api.github.com/users/naumenko-sa/followers","following_url":"https://api.github.com/users/naumenko-sa/following{/other_user}","gists_url":"https://api.github.com/users/naumenko-sa/gists{/gist_id}","starred_url":"https://api.github.com/users/naumenko-sa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/naumenko-sa/subscriptions","organizations_url":"https://api.github.com/users/naumenko-sa/orgs","repos_url":"https://api.github.com/users/naumenko-sa/repos","events_url":"https://api.github.com/users/naumenko-sa/events{/privacy}","received_events_url":"https://api.github.com/users/naumenko-sa/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":23,"created_at":"2016-08-05T19:07:33Z","updated_at":"2016-09-15T16:46:13Z","closed_at":"2016-08-17T12:50:47Z","body":"Hi bcbio developers!\r\n\r\nI have validated RNA-seq variant calling in BCBIO with SRR307898 dataset (GM12878 cell line).\r\nThe precision is 90%. \r\n\r\nIn bcbio-nextgen/bcbio/rnaseq/variation.py I see 3 steps\r\n```\r\ndef rnaseq_gatk_variant_calling(data):\r\n    data = dd.set_deduped_bam(data, dedup_bam(dd.get_work_bam(data), data))\r\n    data = gatk_splitreads(data)\r\n    data = gatk_rnaseq_calling(data)\r\n    return data\r\n```\r\nWhile GATK best practices suggest one more important step: filtering (step 7).\r\n[https://software.broadinstitute.org/gatk/guide/article?id=3891](https://software.broadinstitute.org/gatk/guide/article?id=3891).\r\n\r\nIn my experience it really improves precision at least to 95%.\r\n\r\nCould you include this step into variation.py?\r\n\r\nAlso it would be nice to filter out RNA-editing sites by default.\r\nIt should not be complex:\r\n```\r\nbedtools subtract -header -a input.vcf -b rnaedit.bed >output.vcf\r\n```\r\n\r\nMany thanks,\r\nSN"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/247383943","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1502#issuecomment-247383943","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1502","id":247383943,"user":{"login":"roryk","id":414586,"avatar_url":"https://avatars.githubusercontent.com/u/414586?v=3","gravatar_id":"","url":"https://api.github.com/users/roryk","html_url":"https://github.com/roryk","followers_url":"https://api.github.com/users/roryk/followers","following_url":"https://api.github.com/users/roryk/following{/other_user}","gists_url":"https://api.github.com/users/roryk/gists{/gist_id}","starred_url":"https://api.github.com/users/roryk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roryk/subscriptions","organizations_url":"https://api.github.com/users/roryk/orgs","repos_url":"https://api.github.com/users/roryk/repos","events_url":"https://api.github.com/users/roryk/events{/privacy}","received_events_url":"https://api.github.com/users/roryk/received_events","type":"User","site_admin":false},"created_at":"2016-09-15T16:46:13Z","updated_at":"2016-09-15T16:46:13Z","body":"Hi Sergey,\r\n\r\nSorry about that. If you do a data update, you should get a new version of the RADAR data that is sorted, zipped and indexed, I should have mentioned that. The err:nil error you are seeing is because the new functionality relies on an unreleased version of vcfanno (https://github.com/brentp/vcfanno). I'll bug brent to push a release so we can get that up to date."}}
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