{"action":"created","issue":{"url":"https://api.github.com/repos/hammerlab/guacamole/issues/384","repository_url":"https://api.github.com/repos/hammerlab/guacamole","labels_url":"https://api.github.com/repos/hammerlab/guacamole/issues/384/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/guacamole/issues/384/comments","events_url":"https://api.github.com/repos/hammerlab/guacamole/issues/384/events","html_url":"https://github.com/hammerlab/guacamole/pull/384","id":133867325,"number":384,"title":"Add joint caller","user":{"login":"timodonnell","id":467896,"avatar_url":"https://avatars.githubusercontent.com/u/467896?v=3","gravatar_id":"","url":"https://api.github.com/users/timodonnell","html_url":"https://github.com/timodonnell","followers_url":"https://api.github.com/users/timodonnell/followers","following_url":"https://api.github.com/users/timodonnell/following{/other_user}","gists_url":"https://api.github.com/users/timodonnell/gists{/gist_id}","starred_url":"https://api.github.com/users/timodonnell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timodonnell/subscriptions","organizations_url":"https://api.github.com/users/timodonnell/orgs","repos_url":"https://api.github.com/users/timodonnell/repos","events_url":"https://api.github.com/users/timodonnell/events{/privacy}","received_events_url":"https://api.github.com/users/timodonnell/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":28,"created_at":"2016-02-16T02:35:17Z","updated_at":"2016-02-19T15:57:56Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/hammerlab/guacamole/pulls/384","html_url":"https://github.com/hammerlab/guacamole/pull/384","diff_url":"https://github.com/hammerlab/guacamole/pull/384.diff","patch_url":"https://github.com/hammerlab/guacamole/pull/384.patch"},"body":"This PR starts a germline and somatic multisample variant caller. There is much more to do but it's overdue for me to get some feedback on this and got it integrated into master.\r\n\r\nWhat's implemented:\r\n * Call germline and somatic variants using a likelihood ratio test on individual samples and pooled reads, including indels\r\n * Write out single-sample and multisample VCFs for all calls across all samples with diagnostic info\r\n * Simple unit tests as well as an integration test that runs it on a subset of a real dataset\r\n\r\nWhat is left to do\r\n * Filters (strand bias, evidence in normal, homopolymers, etc.)\r\n * Phasing of variants, including an idea to get better sensitivity from phasing somatic variants with germline hets\r\n * Support for RNA\r\n\r\nOutstanding issues\r\n * Travis still dies while running the integration test. I think it may be running too slowly do to scoverage? Help welcome on this.\n\n<!-- Reviewable:start -->\n[<img src=\"https://reviewable.io/review_button.svg\" height=\"40\" alt=\"Review on Reviewable\"/>](https://reviewable.io/reviews/hammerlab/guacamole/384)\n<!-- Reviewable:end -->\n"},"comment":{"url":"https://api.github.com/repos/hammerlab/guacamole/issues/comments/186275819","html_url":"https://github.com/hammerlab/guacamole/pull/384#issuecomment-186275819","issue_url":"https://api.github.com/repos/hammerlab/guacamole/issues/384","id":186275819,"user":{"login":"timodonnell","id":467896,"avatar_url":"https://avatars.githubusercontent.com/u/467896?v=3","gravatar_id":"","url":"https://api.github.com/users/timodonnell","html_url":"https://github.com/timodonnell","followers_url":"https://api.github.com/users/timodonnell/followers","following_url":"https://api.github.com/users/timodonnell/following{/other_user}","gists_url":"https://api.github.com/users/timodonnell/gists{/gist_id}","starred_url":"https://api.github.com/users/timodonnell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timodonnell/subscriptions","organizations_url":"https://api.github.com/users/timodonnell/orgs","repos_url":"https://api.github.com/users/timodonnell/repos","events_url":"https://api.github.com/users/timodonnell/events{/privacy}","received_events_url":"https://api.github.com/users/timodonnell/received_events","type":"User","site_admin":false},"created_at":"2016-02-19T15:57:56Z","updated_at":"2016-02-19T15:57:56Z","body":"@e5c I was worried that some complex regions of the genome may be generating huge numbers of alleles (and thus generating variants with a big memory footprint for the allelic depth field), so I just pushed a change that adds a `--max-alleles-per-site` option (default=4). Worth giving this one a shot if you are still hitting memory issues on the cluster."}}