{"action":"created","issue":{"url":"https://api.github.com/repos/popgenmethods/smcpp/issues/77","repository_url":"https://api.github.com/repos/popgenmethods/smcpp","labels_url":"https://api.github.com/repos/popgenmethods/smcpp/issues/77/labels{/name}","comments_url":"https://api.github.com/repos/popgenmethods/smcpp/issues/77/comments","events_url":"https://api.github.com/repos/popgenmethods/smcpp/issues/77/events","html_url":"https://github.com/popgenmethods/smcpp/issues/77","id":305747018,"number":77,"title":"Variant quality filter & sequencing error?","user":{"login":"melop","id":1661121,"avatar_url":"https://avatars3.githubusercontent.com/u/1661121?v=4","gravatar_id":"","url":"https://api.github.com/users/melop","html_url":"https://github.com/melop","followers_url":"https://api.github.com/users/melop/followers","following_url":"https://api.github.com/users/melop/following{/other_user}","gists_url":"https://api.github.com/users/melop/gists{/gist_id}","starred_url":"https://api.github.com/users/melop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/melop/subscriptions","organizations_url":"https://api.github.com/users/melop/orgs","repos_url":"https://api.github.com/users/melop/repos","events_url":"https://api.github.com/users/melop/events{/privacy}","received_events_url":"https://api.github.com/users/melop/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-03-15T22:54:34Z","updated_at":"2018-03-16T08:29:42Z","closed_at":"2018-03-15T23:28:09Z","author_association":"NONE","body":"I am wondering what the lowest variant quality in the vcf file is accepted by the vcf2smc command?\r\nOr does it ignore the variant quality field in the vcf?\r\nVery low variant quality may suggest sequencing error. If these are not filtered out, it's likely for smc++ to infer a recent population expansion?\r\n\r\nThanks!\r\nRay"},"comment":{"url":"https://api.github.com/repos/popgenmethods/smcpp/issues/comments/373639847","html_url":"https://github.com/popgenmethods/smcpp/issues/77#issuecomment-373639847","issue_url":"https://api.github.com/repos/popgenmethods/smcpp/issues/77","id":373639847,"user":{"login":"melop","id":1661121,"avatar_url":"https://avatars3.githubusercontent.com/u/1661121?v=4","gravatar_id":"","url":"https://api.github.com/users/melop","html_url":"https://github.com/melop","followers_url":"https://api.github.com/users/melop/followers","following_url":"https://api.github.com/users/melop/following{/other_user}","gists_url":"https://api.github.com/users/melop/gists{/gist_id}","starred_url":"https://api.github.com/users/melop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/melop/subscriptions","organizations_url":"https://api.github.com/users/melop/orgs","repos_url":"https://api.github.com/users/melop/repos","events_url":"https://api.github.com/users/melop/events{/privacy}","received_events_url":"https://api.github.com/users/melop/received_events","type":"User","site_admin":false},"created_at":"2018-03-16T08:29:42Z","updated_at":"2018-03-16T08:29:42Z","author_association":"NONE","body":"Thanks. Should these sites be given in the mask bed file or should they be simply deleted from the VCF (treated as invariant sites)?"}}
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