{"action":"created","issue":{"url":"https://api.github.com/repos/robinandeer/puzzle/issues/34","labels_url":"https://api.github.com/repos/robinandeer/puzzle/issues/34/labels{/name}","comments_url":"https://api.github.com/repos/robinandeer/puzzle/issues/34/comments","events_url":"https://api.github.com/repos/robinandeer/puzzle/issues/34/events","html_url":"https://github.com/robinandeer/puzzle/pull/34","id":111831478,"number":34,"title":"Added an IGV goto URL for the variant view.","user":{"login":"dnil","id":758570,"avatar_url":"https://avatars.githubusercontent.com/u/758570?v=3","gravatar_id":"","url":"https://api.github.com/users/dnil","html_url":"https://github.com/dnil","followers_url":"https://api.github.com/users/dnil/followers","following_url":"https://api.github.com/users/dnil/following{/other_user}","gists_url":"https://api.github.com/users/dnil/gists{/gist_id}","starred_url":"https://api.github.com/users/dnil/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dnil/subscriptions","organizations_url":"https://api.github.com/users/dnil/orgs","repos_url":"https://api.github.com/users/dnil/repos","events_url":"https://api.github.com/users/dnil/events{/privacy}","received_events_url":"https://api.github.com/users/dnil/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-10-16T13:27:01Z","updated_at":"2015-10-18T14:01:06Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/robinandeer/puzzle/pulls/34","html_url":"https://github.com/robinandeer/puzzle/pull/34","diff_url":"https://github.com/robinandeer/puzzle/pull/34.diff","patch_url":"https://github.com/robinandeer/puzzle/pull/34.patch"},"body":"I found this useful when browsing variants locally. Assuming I can open a bam file in IGV somehow, I can jump directly to the right spot from puzzle. The http interface allows loading as well, but then one needs to decide on how/where to put the bam data. https://www.broadinstitute.org/igv/ControlIGV"},"comment":{"url":"https://api.github.com/repos/robinandeer/puzzle/issues/comments/149019101","html_url":"https://github.com/robinandeer/puzzle/pull/34#issuecomment-149019101","issue_url":"https://api.github.com/repos/robinandeer/puzzle/issues/34","id":149019101,"user":{"login":"vasiliosz","id":6449441,"avatar_url":"https://avatars.githubusercontent.com/u/6449441?v=3","gravatar_id":"","url":"https://api.github.com/users/vasiliosz","html_url":"https://github.com/vasiliosz","followers_url":"https://api.github.com/users/vasiliosz/followers","following_url":"https://api.github.com/users/vasiliosz/following{/other_user}","gists_url":"https://api.github.com/users/vasiliosz/gists{/gist_id}","starred_url":"https://api.github.com/users/vasiliosz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vasiliosz/subscriptions","organizations_url":"https://api.github.com/users/vasiliosz/orgs","repos_url":"https://api.github.com/users/vasiliosz/repos","events_url":"https://api.github.com/users/vasiliosz/events{/privacy}","received_events_url":"https://api.github.com/users/vasiliosz/received_events","type":"User","site_admin":false},"created_at":"2015-10-18T14:01:06Z","updated_at":"2015-10-18T14:01:06Z","body":"For the built-in tools (`comp_hets` etc) there is the `--families family1,family2` flag . \r\nFor a general query I think you can use the `--sample-filter` flag: \r\n(more in the [GEMINI manual](https://gemini.readthedocs.org/en/latest/content/querying.html#sample-filter-restrict-a-query-to-specified-samples))\r\n\r\nEx \r\n```\r\ngemini query --sample-filter \"family_id='family101'\"  -q \"select * from variants\" gemini.db \r\n```"}}