{"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":12,"created_at":"2018-03-21T08:08:01Z","updated_at":"2018-03-22T14:04:44Z","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/375317494","html_url":"https://github.com/PapenfussLab/gridss/issues/118#issuecomment-375317494","issue_url":"https://api.github.com/repos/PapenfussLab/gridss/issues/118","id":375317494,"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},"created_at":"2018-03-22T14:04:44Z","updated_at":"2018-03-22T14:04:44Z","author_association":"NONE","body":"\"or give me some details about how to filter the origin somatic vcf\"\r\n《Somatic calls will have the genotype QUAL field set to 0 in the normal. You should also apply a minimum QUAL threshold (threshold depends on your coverage) as just using normal QUAL = 0 will germline calls that just happen to have no coverage in the normal.\r\nSomatic LoH calls will have the genotype QUAL field set to 0 in the tumour (somatic LoH variants occur on somatically deleted haplotypes). 》\r\n@d-cameron \r\ncould you please provide me some details the relationship between Coverage and Qual field set in normal ?for example , if coverage is 1000, Qual should be 0 .\r\n\r\n"}}
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