{"action":"created","issue":{"url":"https://api.github.com/repos/walaj/svaba/issues/34","repository_url":"https://api.github.com/repos/walaj/svaba","labels_url":"https://api.github.com/repos/walaj/svaba/issues/34/labels{/name}","comments_url":"https://api.github.com/repos/walaj/svaba/issues/34/comments","events_url":"https://api.github.com/repos/walaj/svaba/issues/34/events","html_url":"https://github.com/walaj/svaba/issues/34","id":371245164,"node_id":"MDU6SXNzdWUzNzEyNDUxNjQ=","number":34,"title":"Query regarding SV calls","user":{"login":"pwanj","id":43839634,"node_id":"MDQ6VXNlcjQzODM5NjM0","avatar_url":"https://avatars0.githubusercontent.com/u/43839634?v=4","gravatar_id":"","url":"https://api.github.com/users/pwanj","html_url":"https://github.com/pwanj","followers_url":"https://api.github.com/users/pwanj/followers","following_url":"https://api.github.com/users/pwanj/following{/other_user}","gists_url":"https://api.github.com/users/pwanj/gists{/gist_id}","starred_url":"https://api.github.com/users/pwanj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pwanj/subscriptions","organizations_url":"https://api.github.com/users/pwanj/orgs","repos_url":"https://api.github.com/users/pwanj/repos","events_url":"https://api.github.com/users/pwanj/events{/privacy}","received_events_url":"https://api.github.com/users/pwanj/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-10-17T20:04:19Z","updated_at":"2018-10-22T16:28:33Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nI ran svaba on few BAM files (similar samples) . I observed that a SV call is made in some samples and not in others, even though the discordant reads can be seen in the BAM files for all samples in IGV. Is there any filtering criteria or cut-off used to decide when a SV call is made and written to the *sv.vcf files? (Mode: tumor only )\r\n\r\nI would appreciate your help.\r\n\r\nThanks! "},"comment":{"url":"https://api.github.com/repos/walaj/svaba/issues/comments/431887590","html_url":"https://github.com/walaj/svaba/issues/34#issuecomment-431887590","issue_url":"https://api.github.com/repos/walaj/svaba/issues/34","id":431887590,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMTg4NzU5MA==","user":{"login":"pwanj","id":43839634,"node_id":"MDQ6VXNlcjQzODM5NjM0","avatar_url":"https://avatars0.githubusercontent.com/u/43839634?v=4","gravatar_id":"","url":"https://api.github.com/users/pwanj","html_url":"https://github.com/pwanj","followers_url":"https://api.github.com/users/pwanj/followers","following_url":"https://api.github.com/users/pwanj/following{/other_user}","gists_url":"https://api.github.com/users/pwanj/gists{/gist_id}","starred_url":"https://api.github.com/users/pwanj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pwanj/subscriptions","organizations_url":"https://api.github.com/users/pwanj/orgs","repos_url":"https://api.github.com/users/pwanj/repos","events_url":"https://api.github.com/users/pwanj/events{/privacy}","received_events_url":"https://api.github.com/users/pwanj/received_events","type":"User","site_admin":false},"created_at":"2018-10-22T16:28:33Z","updated_at":"2018-10-22T16:28:33Z","author_association":"NONE","body":"![untitled](https://user-images.githubusercontent.com/43839634/47304770-26d10c80-d5ed-11e8-8ad5-71b3df1f2c33.png)\r\n\r\nHere in the above example, the SV call is made for the top sample, but not for the other 2 samples. However, the discordant reads are present in all 3 samples. Please can you tell me why?\r\n\r\nI would appreciate it. Thanks!"}}
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