{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/avocado/issues/167","labels_url":"https://api.github.com/repos/bigdatagenomics/avocado/issues/167/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/avocado/issues/167/comments","events_url":"https://api.github.com/repos/bigdatagenomics/avocado/issues/167/events","html_url":"https://github.com/bigdatagenomics/avocado/pull/167","id":77856861,"number":167,"title":"Work on getting Mutect algorithm up and running","user":{"login":"jstjohn","id":459014,"avatar_url":"https://avatars.githubusercontent.com/u/459014?v=3","gravatar_id":"","url":"https://api.github.com/users/jstjohn","html_url":"https://github.com/jstjohn","followers_url":"https://api.github.com/users/jstjohn/followers","following_url":"https://api.github.com/users/jstjohn/following{/other_user}","gists_url":"https://api.github.com/users/jstjohn/gists{/gist_id}","starred_url":"https://api.github.com/users/jstjohn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jstjohn/subscriptions","organizations_url":"https://api.github.com/users/jstjohn/orgs","repos_url":"https://api.github.com/users/jstjohn/repos","events_url":"https://api.github.com/users/jstjohn/events{/privacy}","received_events_url":"https://api.github.com/users/jstjohn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":13,"created_at":"2015-05-18T23:51:24Z","updated_at":"2015-05-26T20:59:27Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/bigdatagenomics/avocado/pulls/167","html_url":"https://github.com/bigdatagenomics/avocado/pull/167","diff_url":"https://github.com/bigdatagenomics/avocado/pull/167.diff","patch_url":"https://github.com/bigdatagenomics/avocado/pull/167.patch"},"body":"This PR is to track progress and collaborate on an implementation of the MuTect algorithm referenced in #114. "},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/avocado/issues/comments/105663129","html_url":"https://github.com/bigdatagenomics/avocado/pull/167#issuecomment-105663129","issue_url":"https://api.github.com/repos/bigdatagenomics/avocado/issues/167","id":105663129,"user":{"login":"jstjohn","id":459014,"avatar_url":"https://avatars.githubusercontent.com/u/459014?v=3","gravatar_id":"","url":"https://api.github.com/users/jstjohn","html_url":"https://github.com/jstjohn","followers_url":"https://api.github.com/users/jstjohn/followers","following_url":"https://api.github.com/users/jstjohn/following{/other_user}","gists_url":"https://api.github.com/users/jstjohn/gists{/gist_id}","starred_url":"https://api.github.com/users/jstjohn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jstjohn/subscriptions","organizations_url":"https://api.github.com/users/jstjohn/orgs","repos_url":"https://api.github.com/users/jstjohn/repos","events_url":"https://api.github.com/users/jstjohn/events{/privacy}","received_events_url":"https://api.github.com/users/jstjohn/received_events","type":"User","site_admin":false},"created_at":"2015-05-26T20:59:27Z","updated_at":"2015-05-26T20:59:27Z","body":"Just realized something, one Mutect filter is the distance between an allele and an indel in a read. So for example a read with an indel may be filtered out for one allele call adjacent to that indel, but that same read would be included for an allele that is further away on a read. @fnothaft what would you recommend for this? It seems like it might be good to just pass the reads themselves into MuTectGenotyper rather than adding yet another thing to the Allele object and passing that in. "}}