{"action":"created","issue":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2521","repository_url":"https://api.github.com/repos/bcbio/bcbio-nextgen","labels_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2521/labels{/name}","comments_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2521/comments","events_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2521/events","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2521","id":362150457,"node_id":"MDU6SXNzdWUzNjIxNTA0NTc=","number":2521,"title":"somatic variant calling with RNA-seq data ","user":{"login":"deaytan","id":36951030,"node_id":"MDQ6VXNlcjM2OTUxMDMw","avatar_url":"https://avatars2.githubusercontent.com/u/36951030?v=4","gravatar_id":"","url":"https://api.github.com/users/deaytan","html_url":"https://github.com/deaytan","followers_url":"https://api.github.com/users/deaytan/followers","following_url":"https://api.github.com/users/deaytan/following{/other_user}","gists_url":"https://api.github.com/users/deaytan/gists{/gist_id}","starred_url":"https://api.github.com/users/deaytan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deaytan/subscriptions","organizations_url":"https://api.github.com/users/deaytan/orgs","repos_url":"https://api.github.com/users/deaytan/repos","events_url":"https://api.github.com/users/deaytan/events{/privacy}","received_events_url":"https://api.github.com/users/deaytan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-09-20T11:48:49Z","updated_at":"2018-09-27T09:53:58Z","closed_at":null,"author_association":"NONE","body":"In order to call somatic variations using RNA-seq data, do you have any recommended configuration file? And is it fine to do somatic variant calling using RNA-seq data with your variation algorithm? \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/comments/425031096","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2521#issuecomment-425031096","issue_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2521","id":425031096,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNTAzMTA5Ng==","user":{"login":"deaytan","id":36951030,"node_id":"MDQ6VXNlcjM2OTUxMDMw","avatar_url":"https://avatars2.githubusercontent.com/u/36951030?v=4","gravatar_id":"","url":"https://api.github.com/users/deaytan","html_url":"https://github.com/deaytan","followers_url":"https://api.github.com/users/deaytan/followers","following_url":"https://api.github.com/users/deaytan/following{/other_user}","gists_url":"https://api.github.com/users/deaytan/gists{/gist_id}","starred_url":"https://api.github.com/users/deaytan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deaytan/subscriptions","organizations_url":"https://api.github.com/users/deaytan/orgs","repos_url":"https://api.github.com/users/deaytan/repos","events_url":"https://api.github.com/users/deaytan/events{/privacy}","received_events_url":"https://api.github.com/users/deaytan/received_events","type":"User","site_admin":false},"created_at":"2018-09-27T09:53:58Z","updated_at":"2018-09-27T09:53:58Z","author_association":"NONE","body":"Hi,\r\n\r\nThank you very much for your answer. I tried to add variant calling feature into RNA-seq configuration however, I got an error regarding to BED file:\r\n\r\nIOError: Cannot write transcript BED output file /services/tools/bcbio-nextgen/1.0.1/share/genomes/Hsapiens/hg19/rnaseq/ref-transcripts.bed\r\n\r\nMy configuration file was included in these lines under the algorithm title:\r\n\r\n      aligner: star\r\n      quality_format: Standard\r\n      trim_reads: read_through\r\n      adapters: [truseq, polya]\r\n      strandedness: unstranded\r\n      variantcaller: vardict \r\n\r\nIs it the way to call variants for RNA-seq pipeline or am I completely wrong about that?\r\n\r\nAnd for your question, we were originally thinking about subtraction between samples but I think it is not possible with your RNA-seq pipeline I guess. \r\n\r\nIn spite of the fact that, what if I run my RNAseq samples with your variation pipeline which is originally for DNAseq samples. Would I do a huge mistake? \r\n\r\n\r\n\r\n\r\n"}}
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