{"action":"closed","issue":{"url":"https://api.github.com/repos/etal/cnvkit/issues/142","repository_url":"https://api.github.com/repos/etal/cnvkit","labels_url":"https://api.github.com/repos/etal/cnvkit/issues/142/labels{/name}","comments_url":"https://api.github.com/repos/etal/cnvkit/issues/142/comments","events_url":"https://api.github.com/repos/etal/cnvkit/issues/142/events","html_url":"https://github.com/etal/cnvkit/issues/142","id":179997468,"number":142,"title":"Recommendations for SNV VCF files","user":{"login":"holtgrewe","id":521780,"avatar_url":"https://avatars.githubusercontent.com/u/521780?v=3","gravatar_id":"","url":"https://api.github.com/users/holtgrewe","html_url":"https://github.com/holtgrewe","followers_url":"https://api.github.com/users/holtgrewe/followers","following_url":"https://api.github.com/users/holtgrewe/following{/other_user}","gists_url":"https://api.github.com/users/holtgrewe/gists{/gist_id}","starred_url":"https://api.github.com/users/holtgrewe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/holtgrewe/subscriptions","organizations_url":"https://api.github.com/users/holtgrewe/orgs","repos_url":"https://api.github.com/users/holtgrewe/repos","events_url":"https://api.github.com/users/holtgrewe/events{/privacy}","received_events_url":"https://api.github.com/users/holtgrewe/received_events","type":"User","site_admin":false},"labels":[{"id":112211064,"url":"https://api.github.com/repos/etal/cnvkit/labels/question","name":"question","color":"cc317c","default":true},{"id":484598027,"url":"https://api.github.com/repos/etal/cnvkit/labels/vcf","name":"vcf","color":"fbca04","default":false}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-09-29T09:29:29Z","updated_at":"2016-11-20T23:14:23Z","closed_at":"2016-11-20T23:14:23Z","body":"Hi,\n\nwhat are good recommendations for VCF files to put into CNVkit? I did not find anything on this in the manual...\n- Should I use the results of a somatic variant caller such as Mutect or rather \"raw\" variant calls of the tumor only?\n- Should I prefilter this to high-confidence calls, e.g., remove off-target calls and those of low coverage or will cnvkit take care of this?\n\nThanks\n"}}
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