{"action":"created","issue":{"url":"https://api.github.com/repos/Davb06/scripts/issues/1","labels_url":"https://api.github.com/repos/Davb06/scripts/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/Davb06/scripts/issues/1/comments","events_url":"https://api.github.com/repos/Davb06/scripts/issues/1/events","html_url":"https://github.com/Davb06/scripts/issues/1","id":110819282,"number":1,"title":"GATK mm9 vcf file","user":{"login":"lucapinello","id":1081322,"avatar_url":"https://avatars.githubusercontent.com/u/1081322?v=3","gravatar_id":"","url":"https://api.github.com/users/lucapinello","html_url":"https://github.com/lucapinello","followers_url":"https://api.github.com/users/lucapinello/followers","following_url":"https://api.github.com/users/lucapinello/following{/other_user}","gists_url":"https://api.github.com/users/lucapinello/gists{/gist_id}","starred_url":"https://api.github.com/users/lucapinello/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lucapinello/subscriptions","organizations_url":"https://api.github.com/users/lucapinello/orgs","repos_url":"https://api.github.com/users/lucapinello/repos","events_url":"https://api.github.com/users/lucapinello/events{/privacy}","received_events_url":"https://api.github.com/users/lucapinello/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-10-10T22:00:41Z","updated_at":"2015-10-13T15:25:28Z","closed_at":null,"body":"Hi!\r\n\r\nI saw your nice set of scripts. This is really nice.\r\n\r\nI am trying to play with GATK with mm9 reference genome, do you mind to share the file:\r\nmm9_snp132-sort-filtered.vcf referenced in your pipeline?\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/Davb06/scripts/issues/comments/147749611","html_url":"https://github.com/Davb06/scripts/issues/1#issuecomment-147749611","issue_url":"https://api.github.com/repos/Davb06/scripts/issues/1","id":147749611,"user":{"login":"Davb06","id":7728186,"avatar_url":"https://avatars.githubusercontent.com/u/7728186?v=3","gravatar_id":"","url":"https://api.github.com/users/Davb06","html_url":"https://github.com/Davb06","followers_url":"https://api.github.com/users/Davb06/followers","following_url":"https://api.github.com/users/Davb06/following{/other_user}","gists_url":"https://api.github.com/users/Davb06/gists{/gist_id}","starred_url":"https://api.github.com/users/Davb06/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Davb06/subscriptions","organizations_url":"https://api.github.com/users/Davb06/orgs","repos_url":"https://api.github.com/users/Davb06/repos","events_url":"https://api.github.com/users/Davb06/events{/privacy}","received_events_url":"https://api.github.com/users/Davb06/received_events","type":"User","site_admin":false},"created_at":"2015-10-13T15:25:28Z","updated_at":"2015-10-13T15:25:28Z","body":"Hi Luca,\n\nI'd be happy to.  I had to upload it to Box due to its size.  click here:\n\nhttps://upenn.box.com/s/163s76hee5lc8hhed37bjmm937ugu1w9\n\n\nThe GATK version we use (v. 3.1-1-g07a4bf8) doesn't work with the large\nindels in dbSNP.  So the \"filtered\" in the file name refers to removal of\none particular 16 bp del that GATK wouldn't process (rs4230749).  It is\nalso sorted by Chromosome per GATK's requirements (chr1, chr2, chr3...).\nI have not had any issue with the file, but let me know if you do.\n\nOn Sat, Oct 10, 2015 at 6:00 PM, Luca Pinello <notifications@github.com>\nwrote:\n\n> Hi!\n>\n> I saw your nice set of scripts. This is really nice.\n>\n> I am trying to play with GATK with mm9 reference genome, do you mind to\n> share the file:\n> mm9_snp132-sort-filtered.vcf referenced in your pipeline?\n>\n> Thanks!\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/Davb06/scripts/issues/1>.\n>\n"}}