{"id":24360473,"url":"https://github.com/simonsfoundation/anno-dbnsfp","last_synced_at":"2026-04-19T23:34:08.875Z","repository":{"id":98237108,"uuid":"55801618","full_name":"simonsfoundation/anno-dbnsfp","owner":"simonsfoundation","description":null,"archived":false,"fork":false,"pushed_at":"2017-03-31T14:16:51.000Z","size":16,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-01-18T21:32:28.271Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/simonsfoundation.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-04-08T18:41:26.000Z","updated_at":"2018-02-10T03:39:08.000Z","dependencies_parsed_at":"2023-05-18T20:45:38.893Z","dependency_job_id":null,"html_url":"https://github.com/simonsfoundation/anno-dbnsfp","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fanno-dbnsfp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fanno-dbnsfp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fanno-dbnsfp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fanno-dbnsfp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/simonsfoundation","download_url":"https://codeload.github.com/simonsfoundation/anno-dbnsfp/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243188204,"owners_count":20250452,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-01-18T21:29:52.261Z","updated_at":"2025-12-26T00:27:35.563Z","avatar_url":"https://github.com/simonsfoundation.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## _anno-dbnsfp_\n\nAnnotate non-synonymous SNPs with values found in [dbNSFP](https://sites.google.com/site/jpopgen/dbNSFP).\n    \n### Installation and usage for running on Simons Foundation/Flatiron Institute cluster. \n\n[sqlite3](http://www.sqlite.org/download.html) must be in your PATH.\n\n```\npip install --user git+git://github.com/simonsfoundation/anno-dbnsfp.git\nexport PATH=$PATH:~/.local/bin\n```\n\nFor help\n```\nanno-dbnsfp.py -h\n```\n\nCreate an input file with mutations to be annotated.\n```\necho 'CHROM,POS,ID,REF,ALT,GENE\n    13,23909440,.,G,A,SACS\n    21,35144452,.,G,A,ITSN1\n    1,180235688,.,G,A,LHX4\n    7,73731910,.,C,T,CLIP2\n    16,3820881,.,G,A,CREBBP\n    3,113508666,.,A,G,ATP6V1A\n    7,148512615,.,T,C,EZH2\n    11,8111646,.,A,C,TUB\n    3,21606142,.,G,T,ZNF385D\n    9,37015066,.,T,A,PAX5\n    2,223917672,.,G,A,KCNE4\n    16,71318883,.,T,C,CMTR2\n    18,21331038,.,A,G,LAMA3\n    17,78831603,.,G,A,RPTOR\n    12,49334805,.,A,G,RP11-302B13.5\n    5,145603023,.,C,T,RBM27\n    10,104596833,rs104894138,G,A,CYP17A1\n    12,120436359,.,G,A,CCDC64\n    1,213145953,.,C,T,VASH2' \u003e test_mutations.csv\n    \n```\n\nAnnotate\n\n```\nanno-dbnsfp.py --genome_build=hg19 --input_delim=csv test_mutations.csv\ncat test_mutations.csv.ann.tsv\n```\n\nTo see all available dbNSFP columns\n```\nanno-dbnsfp.py -p test_mutations.csv \n```\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimonsfoundation%2Fanno-dbnsfp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsimonsfoundation%2Fanno-dbnsfp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimonsfoundation%2Fanno-dbnsfp/lists"}