{"id":20386920,"url":"https://github.com/cmdcolin/jbrowse-plugin-gwas","last_synced_at":"2025-09-12T10:34:12.385Z","repository":{"id":57279797,"uuid":"339564531","full_name":"cmdcolin/jbrowse-plugin-gwas","owner":"cmdcolin","description":null,"archived":false,"fork":false,"pushed_at":"2025-02-05T18:42:35.000Z","size":865,"stargazers_count":4,"open_issues_count":7,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-12T09:54:01.625Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"TypeScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cmdcolin.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":null,"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}},"created_at":"2021-02-17T00:00:41.000Z","updated_at":"2025-02-05T18:42:39.000Z","dependencies_parsed_at":"2024-11-15T02:41:30.934Z","dependency_job_id":"02add9d2-66ce-4b7d-b222-f60b39659f4d","html_url":"https://github.com/cmdcolin/jbrowse-plugin-gwas","commit_stats":{"total_commits":33,"total_committers":1,"mean_commits":33.0,"dds":0.0,"last_synced_commit":"75144626660b6313fd0b951cc71c80b05b2c32d6"},"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-gwas","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-gwas/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-gwas/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-gwas/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdcolin","download_url":"https://codeload.github.com/cmdcolin/jbrowse-plugin-gwas/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248550634,"owners_count":21122932,"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":"2024-11-15T02:41:23.841Z","updated_at":"2025-04-12T09:54:09.536Z","avatar_url":"https://github.com/cmdcolin.png","language":"TypeScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# jbrowse-plugin-gwas\n\nPlugin for displaying GWAS results such as manhattan plot renderings\n\n## Screenshot\n\n![](img/1.png) ![](img/2.png)\n\n## Data format\n\njbrowse-plugin-gwas will render any features with a \"score\". A common format is\na BED-like file, perhaps with tabix added. Example with plain BED, where the\nscore is in column 5\n\n```\nchr22 1000 5000 rs123 84.141\nchr22 2000 6000 rs456 40.12312\n```\n\nSometimes, the file format is not a strict BED but something with just one\ncoordinate instead of a start and end. Example with BED-like data (only one\ncoordinate column)\n\n```\n#chrom  pos     rsid    ref     alt     neg_log_pvalue  beta    stderr_beta     alt_allele_freq\n1       721290  rs12565286      G       C       0.275233        .       .       .\n1       752566  rs3094315       G       A       0.0315638       .       .       .\n1       775659  rs2905035       A       G       0.183626        .       .       .\n1       777122  rs2980319       A       T       0.207258        .       .       .\n1       779322  rs4040617       A       G       0.0326393       .       .       .\n1       780785  rs2977612       T       A       0.0225965       .       .       .\n```\n\nThis file format can be indexed using tabix with something BED-like\n\n```\ntabix -0 -b 2 -s 1 -e 2 -f out.bed.gz\n```\n\nThe beginning (-b) and end (-e) coordinates of the features are set to the same\ncolumn (2), and the sequence column (-s) is 1. Also assumes zero-based\ncoordinates (-0)\n\nNote that this is just one format that can be used for the plugin, any adapter\ncan be used that provides features with a score attribute, and it assumes the\nscore is already -log10(p) transformed (this means if your file has raw\np-values, you may need to modify them or add a -log10(p) to the file)\n\n## Example config\n\nThe below config uses the \"scoreColumn\" attribute to set neg_log_pvalue (as seen\nin above section) to be the score that is plotted\n\n```json\n{\n  \"type\": \"FeatureTrack\",\n  \"trackId\": \"gwas_track\",\n  \"name\": \"GWAS\",\n  \"category\": [\"Annotation\"],\n  \"assemblyNames\": [\"hg19\"],\n  \"adapter\": {\n    \"type\": \"BedTabixAdapter\",\n    \"scoreColumn\": \"neg_log_pvalue\",\n    \"bedGzLocation\": {\n      \"uri\": \"https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gwas/summary_stats.txt.gz\"\n    },\n    \"index\": {\n      \"location\": {\n        \"uri\": \"https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gwas/summary_stats.txt.gz.tbi\"\n      },\n      \"indexType\": \"TBI\"\n    }\n  },\n  \"displays\": [\n    {\n      \"displayId\": \"gwas_display\",\n      \"type\": \"LinearManhattanDisplay\"\n    }\n  ]\n}\n```\n\n## Usage in jbrowse-web\n\nAdd to the \"plugins\" of your JBrowse Web config. The unpkg CDN should be stable,\nor you can download the js file to your server\n\n```json\n{\n  \"plugins\": [\n    {\n      \"name\": \"GWAS\",\n      \"url\": \"https://unpkg.com/jbrowse-plugin-gwas/dist/jbrowse-plugin-gwas.umd.production.min.js\"\n    }\n  ]\n}\n```\n\nThis plugin is currently quite basic, and there is no mouseover interactivity or\ndrawn labels on features\n\n#### Demo\n\nhttps://jbrowse.org/code/jb2/main/index.html?config=https%3A%2F%2Funpkg.com%2Fjbrowse-plugin-gwas%2Fdist%2Fconfig.json\u0026session=share-iehjT6AoHd\u0026password=lZS7v\n\n### For use in jbrowse/react-linear-genome-view\n\nSee [DEVELOPMENT](DEVELOPMENT.md)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fjbrowse-plugin-gwas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdcolin%2Fjbrowse-plugin-gwas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fjbrowse-plugin-gwas/lists"}