{"id":19857034,"url":"https://github.com/griffithlab/igvnav","last_synced_at":"2025-10-24T13:45:55.283Z","repository":{"id":78129837,"uuid":"83464784","full_name":"griffithlab/igvnav","owner":"griffithlab","description":null,"archived":false,"fork":false,"pushed_at":"2018-01-19T23:35:38.000Z","size":76533,"stargazers_count":15,"open_issues_count":9,"forks_count":3,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-07-10T07:01:05.894Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/griffithlab.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2017-02-28T18:17:25.000Z","updated_at":"2022-01-03T07:46:11.000Z","dependencies_parsed_at":"2023-02-24T02:00:20.446Z","dependency_job_id":null,"html_url":"https://github.com/griffithlab/igvnav","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/griffithlab/igvnav","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Figvnav","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Figvnav/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Figvnav/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Figvnav/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/igvnav/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Figvnav/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280806800,"owners_count":26394450,"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","status":"online","status_checked_at":"2025-10-24T02:00:06.418Z","response_time":73,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-11-12T14:17:16.689Z","updated_at":"2025-10-24T13:45:55.278Z","avatar_url":"https://github.com/griffithlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## PURPOSE\n\nIGVNavigator (IGVNav) is a tool that was developed to assist in analyzing \nvariants during manual review. Its input is a text file with variant \ncoordinates and its output provides an annotation of these variant \ncoordinates. This annotation includes the call (i.e. somatic, germline, \nambiguous, or fail), tags to provide additional information if a variant \nis called ambiguous or fail, and a notes section for free text\n\n## DOWNLOAD\n\nSteps to download IGVNav for Mac:\n\n1) Download [IGVNav.zip](https://github.com/griffithlab/igvnav/raw/master/dist/IGVNav.zip)\n\n2) Unzip File\n\n3) Add unzipped file to Applications/ folder.\n\n\n\n## INSTRUCTIONS FOR USE\n\n1) Open IGV\n\n2) Load session file (e.g. .bam files)\n\n3) open IGVNav applicaiton \n\n4) IGVNav app will prompt you to open a manual review file.\n\n5) Open a manual review file whereby the format of this file\nis a TSV file with columns:\n   \n```Chromosome, Start, Stop, Reference, Variant, Call, Tags, Notes```\n\n6) The first six columns (Chromosome, Start, Stop, Reference, and Variant)\nshould be filled-out and the remaining columns will be blank.\n\n*NOTE: The column names do not have to match exactly the above, but they do\nhave to be the correct data in the same column order.*\n\n7) Navigate through the manual review file using the arrows on the \nIGVNav interface.\n\n8) Ensure that coordinates on IGVNav interface match the IGV interface.\n\n9) Select a Call for each variant based on support for variant.\n\n10) Select various Tags for each variant if variant is labeled\nas ambiguous or fail.\n\n11) Input any notes required in the free-text box.\n\n12) Periodically save the manual review file to ensure that calls\nare recorded. Be sure to save the manual review file prior to closing\nthe IGVNav session.\n\n## EXAMPLE INTERFACE\n\n![alt text](https://github.com/griffithlab/igvnav/blob/master/IGVNav_interface.png)\n\n\n## INSTRUCTIONS FOR DEVELOPING\n\n1) clone the repo/ sub-folder\n\n2) Edit IGVNav.py\n\nTo build, you will need to install wxPython and py2applet:\n$ python setup.py py2app\n\nApp will be placed in dist/ sub-directory of the repository\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Figvnav","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Figvnav","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Figvnav/lists"}