{"action":"created","issue":{"url":"https://api.github.com/repos/PapenfussLab/gridss/issues/118","repository_url":"https://api.github.com/repos/PapenfussLab/gridss","labels_url":"https://api.github.com/repos/PapenfussLab/gridss/issues/118/labels{/name}","comments_url":"https://api.github.com/repos/PapenfussLab/gridss/issues/118/comments","events_url":"https://api.github.com/repos/PapenfussLab/gridss/issues/118/events","html_url":"https://github.com/PapenfussLab/gridss/issues/118","id":307149792,"number":118,"title":"which R version should I install  and what's  the detailed process of somatic.R？","user":{"login":"WinterLi1993","id":10543236,"avatar_url":"https://avatars3.githubusercontent.com/u/10543236?v=4","gravatar_id":"","url":"https://api.github.com/users/WinterLi1993","html_url":"https://github.com/WinterLi1993","followers_url":"https://api.github.com/users/WinterLi1993/followers","following_url":"https://api.github.com/users/WinterLi1993/following{/other_user}","gists_url":"https://api.github.com/users/WinterLi1993/gists{/gist_id}","starred_url":"https://api.github.com/users/WinterLi1993/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/WinterLi1993/subscriptions","organizations_url":"https://api.github.com/users/WinterLi1993/orgs","repos_url":"https://api.github.com/users/WinterLi1993/repos","events_url":"https://api.github.com/users/WinterLi1993/events{/privacy}","received_events_url":"https://api.github.com/users/WinterLi1993/received_events","type":"User","site_admin":false},"labels":[{"id":223188291,"url":"https://api.github.com/repos/PapenfussLab/gridss/labels/help%20wanted","name":"help wanted","color":"159818","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-03-21T08:08:01Z","updated_at":"2018-03-22T10:14:57Z","closed_at":null,"author_association":"NONE","body":"Hi，\r\n   I have tried R 3.4.4 version, but can not install the  R dependencies  of Gridss ?\r\n   could you please provide  the python version of somatic.R at the \"example\" folder  ?  or  give me some details about how to filter  the origin somatic vcf  . \r\nthank you !"},"comment":{"url":"https://api.github.com/repos/PapenfussLab/gridss/issues/comments/375245592","html_url":"https://github.com/PapenfussLab/gridss/issues/118#issuecomment-375245592","issue_url":"https://api.github.com/repos/PapenfussLab/gridss/issues/118","id":375245592,"user":{"login":"d-cameron","id":6036536,"avatar_url":"https://avatars3.githubusercontent.com/u/6036536?v=4","gravatar_id":"","url":"https://api.github.com/users/d-cameron","html_url":"https://github.com/d-cameron","followers_url":"https://api.github.com/users/d-cameron/followers","following_url":"https://api.github.com/users/d-cameron/following{/other_user}","gists_url":"https://api.github.com/users/d-cameron/gists{/gist_id}","starred_url":"https://api.github.com/users/d-cameron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/d-cameron/subscriptions","organizations_url":"https://api.github.com/users/d-cameron/orgs","repos_url":"https://api.github.com/users/d-cameron/repos","events_url":"https://api.github.com/users/d-cameron/events{/privacy}","received_events_url":"https://api.github.com/users/d-cameron/received_events","type":"User","site_admin":false},"created_at":"2018-03-22T10:14:57Z","updated_at":"2018-03-22T10:14:57Z","author_association":"MEMBER","body":"\r\nfor somatic calling :\r\n> the two breakpoints should be : chr1: 154142762 ,chr6:117642093, but I check the gridss result ,I got these result :\r\n> chr1\t154142762 gridss15_2002o\tA\t]chr6:117642092]A 52712.28\tNO_ASSEMBLY\r\n> chr6\t117642092\tgridss15_2002h\tC\tC[chr1:154142762[\t49799.37\tNO_ASSEMBLY\r\n> the position is less than 1bp ,,,,the gridss result is wrong ??\r\n\r\nThe GRIDSS result is correct. I strongly recommend reading Section 5.4 of the [VCF file format specifications](https://samtools.github.io/hts-specs/VCFv4.3.pdf) as that describes the VCF breakpoint notation used by GRIDSS."}}
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