{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/253","repository_url":"https://api.github.com/repos/arq5x/lumpy-sv","labels_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/253/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/253/comments","events_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/253/events","html_url":"https://github.com/arq5x/lumpy-sv/issues/253","id":340056299,"node_id":"MDU6SXNzdWUzNDAwNTYyOTk=","number":253,"title":"Filter VCF Prior to Running SVTyper","user":{"login":"andrewSharo","id":13205434,"node_id":"MDQ6VXNlcjEzMjA1NDM0","avatar_url":"https://avatars2.githubusercontent.com/u/13205434?v=4","gravatar_id":"","url":"https://api.github.com/users/andrewSharo","html_url":"https://github.com/andrewSharo","followers_url":"https://api.github.com/users/andrewSharo/followers","following_url":"https://api.github.com/users/andrewSharo/following{/other_user}","gists_url":"https://api.github.com/users/andrewSharo/gists{/gist_id}","starred_url":"https://api.github.com/users/andrewSharo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrewSharo/subscriptions","organizations_url":"https://api.github.com/users/andrewSharo/orgs","repos_url":"https://api.github.com/users/andrewSharo/repos","events_url":"https://api.github.com/users/andrewSharo/events{/privacy}","received_events_url":"https://api.github.com/users/andrewSharo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2018-07-11T01:03:43Z","updated_at":"2018-07-13T19:58:05Z","closed_at":null,"author_association":"NONE","body":"Hi Ryan,\r\nI'm getting a very large number of SVs in my vcf (~10^6) after running lumpyexpress on a single sample. SVTyper runs very slowly, so I'm looking to filter my vcf prior to running SVTyper. Do you recommend filtering by SU? Filtering for SU > 20 gives ~20,000 SVs which is more manageable. Do you think I may be losing a lot of real calls by doing this?  Should I focus instead on calls that have both split read and paired-end read support?\r\n\r\nAs a side note, do you think running lumpy jointly on multiple samples will help reduce the number of SVs per sample? I have about 100 samples, but have been running them individually.\r\nBest, Andrew"},"comment":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/comments/404937868","html_url":"https://github.com/arq5x/lumpy-sv/issues/253#issuecomment-404937868","issue_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/253","id":404937868,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNDkzNzg2OA==","user":{"login":"andrewSharo","id":13205434,"node_id":"MDQ6VXNlcjEzMjA1NDM0","avatar_url":"https://avatars2.githubusercontent.com/u/13205434?v=4","gravatar_id":"","url":"https://api.github.com/users/andrewSharo","html_url":"https://github.com/andrewSharo","followers_url":"https://api.github.com/users/andrewSharo/followers","following_url":"https://api.github.com/users/andrewSharo/following{/other_user}","gists_url":"https://api.github.com/users/andrewSharo/gists{/gist_id}","starred_url":"https://api.github.com/users/andrewSharo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrewSharo/subscriptions","organizations_url":"https://api.github.com/users/andrewSharo/orgs","repos_url":"https://api.github.com/users/andrewSharo/repos","events_url":"https://api.github.com/users/andrewSharo/events{/privacy}","received_events_url":"https://api.github.com/users/andrewSharo/received_events","type":"User","site_admin":false},"created_at":"2018-07-13T19:58:05Z","updated_at":"2018-07-13T19:58:05Z","author_association":"NONE","body":"Sorry for the slow response. Depending on how it's calculated, read depth is 48 or 51."}}
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