{"action":"created","issue":{"url":"https://api.github.com/repos/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/13","labels_url":"https://api.github.com/repos/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/13/comments","events_url":"https://api.github.com/repos/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/13/events","html_url":"https://github.com/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/13","id":99096876,"number":13,"title":"Enhance VCF to include \"Predicted impact\"","user":{"login":"eweitz","id":1334561,"avatar_url":"https://avatars.githubusercontent.com/u/1334561?v=3","gravatar_id":"","url":"https://api.github.com/users/eweitz","html_url":"https://github.com/eweitz","followers_url":"https://api.github.com/users/eweitz/followers","following_url":"https://api.github.com/users/eweitz/following{/other_user}","gists_url":"https://api.github.com/users/eweitz/gists{/gist_id}","starred_url":"https://api.github.com/users/eweitz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eweitz/subscriptions","organizations_url":"https://api.github.com/users/eweitz/orgs","repos_url":"https://api.github.com/users/eweitz/repos","events_url":"https://api.github.com/users/eweitz/events{/privacy}","received_events_url":"https://api.github.com/users/eweitz/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"nicovbing","id":13243346,"avatar_url":"https://avatars.githubusercontent.com/u/13243346?v=3","gravatar_id":"","url":"https://api.github.com/users/nicovbing","html_url":"https://github.com/nicovbing","followers_url":"https://api.github.com/users/nicovbing/followers","following_url":"https://api.github.com/users/nicovbing/following{/other_user}","gists_url":"https://api.github.com/users/nicovbing/gists{/gist_id}","starred_url":"https://api.github.com/users/nicovbing/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nicovbing/subscriptions","organizations_url":"https://api.github.com/users/nicovbing/orgs","repos_url":"https://api.github.com/users/nicovbing/repos","events_url":"https://api.github.com/users/nicovbing/events{/privacy}","received_events_url":"https://api.github.com/users/nicovbing/received_events","type":"User","site_admin":false},"milestone":null,"comments":4,"created_at":"2015-08-05T01:33:38Z","updated_at":"2015-08-17T18:01:32Z","closed_at":null,"body":"Implement @zmartine's proposal to enhance SnpEff's default impact values for each variant with a new \"predicted impact\" that accounts for significant changes in hydrophobicity, etc.\r\n\r\nInput:\r\n- _VCF file annotated by SnpEff_.  This file will be output by the code pushed for [Issue 7](https://github.com/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/7)\r\n\r\nOutput:\r\n- _VCF file with enhanced annotation_.  The output VCF files should include a \"Predicted impact\" column for each variant reports any reclassification of SnpEff's default impact values.  This would be an additional field in the INFO column.\r\n\r\nThis output will be used as input to the VCF filtering being implemented by @nicovbing in [Issue 8](https://github.com/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/8)."},"comment":{"url":"https://api.github.com/repos/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/comments/131910544","html_url":"https://github.com/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/13#issuecomment-131910544","issue_url":"https://api.github.com/repos/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/issues/13","id":131910544,"user":{"login":"nicovbing","id":13243346,"avatar_url":"https://avatars.githubusercontent.com/u/13243346?v=3","gravatar_id":"","url":"https://api.github.com/users/nicovbing","html_url":"https://github.com/nicovbing","followers_url":"https://api.github.com/users/nicovbing/followers","following_url":"https://api.github.com/users/nicovbing/following{/other_user}","gists_url":"https://api.github.com/users/nicovbing/gists{/gist_id}","starred_url":"https://api.github.com/users/nicovbing/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nicovbing/subscriptions","organizations_url":"https://api.github.com/users/nicovbing/orgs","repos_url":"https://api.github.com/users/nicovbing/repos","events_url":"https://api.github.com/users/nicovbing/events{/privacy}","received_events_url":"https://api.github.com/users/nicovbing/received_events","type":"User","site_admin":false},"created_at":"2015-08-17T18:01:32Z","updated_at":"2015-08-17T18:01:32Z","body":"@eweitz \r\nSorry the command is:\r\n\r\n Rscript script_to_filter_VCF_impact.R YOUR_FILE_oneperline.vcf"}}