{"action":"created","issue":{"url":"https://api.github.com/repos/pmelsted/pizzly/issues/19","repository_url":"https://api.github.com/repos/pmelsted/pizzly","labels_url":"https://api.github.com/repos/pmelsted/pizzly/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/pmelsted/pizzly/issues/19/comments","events_url":"https://api.github.com/repos/pmelsted/pizzly/issues/19/events","html_url":"https://github.com/pmelsted/pizzly/issues/19","id":252098138,"number":19,"title":"pizzly missing a fusion from SRR1659964","user":{"login":"roryk","id":414586,"avatar_url":"https://avatars2.githubusercontent.com/u/414586?v=4","gravatar_id":"","url":"https://api.github.com/users/roryk","html_url":"https://github.com/roryk","followers_url":"https://api.github.com/users/roryk/followers","following_url":"https://api.github.com/users/roryk/following{/other_user}","gists_url":"https://api.github.com/users/roryk/gists{/gist_id}","starred_url":"https://api.github.com/users/roryk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roryk/subscriptions","organizations_url":"https://api.github.com/users/roryk/orgs","repos_url":"https://api.github.com/users/roryk/repos","events_url":"https://api.github.com/users/roryk/events{/privacy}","received_events_url":"https://api.github.com/users/roryk/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-08-22T21:42:06Z","updated_at":"2017-08-23T13:03:58Z","closed_at":null,"body":"Hi Pall,\r\n\r\nThanks for making pizzly. I've been working on adding support for it and some other fast fusion callers to bcbio and have been seeing if I can figure out some way of filtering the fusions to get a cleaner set. Just running the defaults, pizzly is missing the TMPRSS2:ETV1 fusion in the SRR1659964 dataset from the preprint. It shows up in the unfiltered JSON file with some support though, but not the filtered one. Do you have some suggestions for some settings to get this to be identified? How are the transcripts filtered? Thanks! I have run pizzly on the entire fusion dilution series in that dataset if that would be helpful for you all.\r\n\r\n```\r\n        fusion      tpm known\r\n         <chr>    <dbl> <lgl>\r\n1     EML4:ALK 1.762218  TRUE\r\n2   ETV6:NTRK3 5.117153  TRUE\r\n3   BRD4:NUTM1 1.345507  TRUE\r\n4    HOOK3:RET 3.747249  TRUE\r\n5   EWSR1:ATF1 2.092241  TRUE\r\n6 TMPRSS2:ETV1 0.000000  TRUE\r\n7   AKAP9:BRAF 3.046220  TRUE\r\n8    CD74:ROS1 5.370045  TRUE\r\n9   EWSR1:FLI1 1.452139  TRUE\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/pmelsted/pizzly/issues/comments/324323454","html_url":"https://github.com/pmelsted/pizzly/issues/19#issuecomment-324323454","issue_url":"https://api.github.com/repos/pmelsted/pizzly/issues/19","id":324323454,"user":{"login":"roryk","id":414586,"avatar_url":"https://avatars2.githubusercontent.com/u/414586?v=4","gravatar_id":"","url":"https://api.github.com/users/roryk","html_url":"https://github.com/roryk","followers_url":"https://api.github.com/users/roryk/followers","following_url":"https://api.github.com/users/roryk/following{/other_user}","gists_url":"https://api.github.com/users/roryk/gists{/gist_id}","starred_url":"https://api.github.com/users/roryk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roryk/subscriptions","organizations_url":"https://api.github.com/users/roryk/orgs","repos_url":"https://api.github.com/users/roryk/repos","events_url":"https://api.github.com/users/roryk/events{/privacy}","received_events_url":"https://api.github.com/users/roryk/received_events","type":"User","site_admin":false},"created_at":"2017-08-23T13:03:58Z","updated_at":"2017-08-23T13:03:58Z","body":"I've been working a little bit on filtering the calls from pizzly-- if you use the blacklist genes from FusionMap to filter the calls (http://www.omicsoft.com/downloads/fusion/filtering/GeneList_v1.txt) you can dump maybe 10% of the calls. I created a blacklist filter of overlapping genes here (https://github.com/roryk/fusion-gene-blacklist) which doesn't filter any of the calls but is probably useful to check against anyway. The family filter from FusionMap (http://www.omicsoft.com/downloads/fusion/filtering/GeneFamilyList_v1.txt) doesn't do much on this dataset, it just filters out a couple of the pairs."}}
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