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You might want to check out the following repositories as well:\n\n- HiGlass viewer: https://github.com/higlass/higlass\n- HiGlass server: https://github.com/higlass/higlass-server\n- HiGlass docker: https://github.com/higlass/higlass-docker\n\n## Installation\n \n```\nnpm install higlass-gnomad\n```\n\n## Data preparation\n\nThis track uses vcf files as input data. Here is an example of entries that can be consumed by this track:\n\n```\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\nchr21   5030240 rs1185110752    AC      A       .       PASS    AC=16;AN=3778;AF=0.00423504;AF_popmax=0.0296296\nchr21   5030242 .       C       T       .       AC0;AS_VQSR     AC=0;AN=3832;AF=0.00000\nchr21   5030249 .       T       C       .       AC0;AS_VQSR     AC=0;AN=4630;AF=0.00000\nchr21   5030253 rs1486393480    G       T       .       AS_VQSR AC=1;AN=5170;AF=0.000193424;AF_popmax=0.000426621\nchr21   5030262 .       C       A       .       AC0;AS_VQSR     AC=0;AN=6230;AF=0.00000\nchr21   5030275 .       A       G       .       AC0;AS_VQSR     AC=0;AN=7910;AF=0.00000\n```\nNote that `AC` (allele count),`AN` (allele number) and `AF` (allele frequency) is required in the INFO column.\n\nThe track can also display GnomAD SV (structural variants) data. The entries in the vcf file have to be in the following form\n\n```\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\nchr3\t146453963\tnssv16051216  T \u003cINS\u003e .\t.\tAC=1;AF=4.6e-05;AN=21694;END=146453963;SVLEN=281;SVTYPE=INS\nchr3\t146480766\tnssv15885393\tC\t\u003cDEL\u003e\t.\t.\tAC=36;AF=0.001659;AN=21694;END=146481132;SVLEN=-367;SVTYPE=DEL\nchr3\t146485150\tnssv15972036\tC\t\u003cDUP\u003e\t.\t.\tAC=2;AF=9.2e-05;AN=21694;END=146513435;SVLEN=28286;SVTYPE=DUP\nchr3\t146501411\tnssv15885394\tT\t\u003cDEL\u003e\t.\t.\tAC=38;AF=0.001779;AN=21358;END=146502039;SVLEN=-629;SVTYPE=DEL\n```\n\n\n## Usage\n\nThe live script can be found at:\n\n- https://unpkg.com/higlass-gnomad/dist/higlass-gnomad.min.js\n\n\n### Client\n\n1. Load this track before the HiGlass core script. For example:\n\n```\n\u003cscript src=\"/higlass-gnomad.js\"\u003e\u003c/script\u003e\n\u003cscript src=\"hglib.js\"\u003e\u003c/script\u003e\n\n\u003cscript\u003e\n  ...\n\u003c/script\u003e\n```\n\n### Options\nThe following options are available:\n```\n{\n  \"uid\": \"some_uid\",\n  \"type\": \"gnomad\",\n  \"options\": {\n    \"colorScale\": [\n      // Variant, Insertion, Deletion, Inversion, Duplication\n      [0.3, 0.3, 0.3, 0.6],\n      [0.6, 0.6, 0.0, 0.7],\n      [1, 0.0, 0.0, 0.55],\n      [0.68, 0.23, 0.87, 0.8],\n      [0.27, 0.64, 0.09, 0.8]\n    ],\n    \"showMousePosition\": false,\n    \"variantHeight\": 12, // Height of the rectangles\n    \"maxTileWidth\": 2e5 // Determines how far the user can zoom out before data loading stops\n  },\n  \"data\": {\n    \"type\": \"vcf\",\n    \"vcfUrl\": \"https://url_to_your_vcf/gnomad.vcf.gz\",\n    \"tbiUrl\": \"https://url_to_your_vcf/gnomad.vcf.gz.tbi\",\n    \"chromSizesUrl\": \"https://url_to_your_chromsize_file/chrom.sizes\",\n  },\n  \"width\": 768,\n  \"height\": 200\n}\n```\n\n### ECMAScript Modules (ESM)\n\nWe also build out ES modules for usage by applications who may need to import or use `higlass-gnomad` as a component.\n\nWhenever there is a statement such as the following, assuming `higlass-gnomad` is in your node_modules folder:\n```javascript\nimport { GnomadTrack } from 'higlass-gnomad';\n```\n\nThen GnomadTrack would automatically be imported from the `./es` directory (set via package.json's `\"module\"` value). \n\n## Support\n\nFor questions, please either open an issue or ask on the HiGlass Slack channel at http://bit.ly/higlass-slack\n\n## Development\n\n### Installation\n\n```bash\n$ git clone https://github.com/higlass/higlass-gnomad.git\n$ cd higlass-gnomad\n$ npm install\n```\nIf you have a local copy of higlass, you can then run this command in the higlass-gnomad directory:\n\n```bash\nnpm link higlass\n```\n\n### Commands\n\n - **Developmental server**: `npm start`\n - **Production build**: `npm run build`\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-gnomad","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhiglass%2Fhiglass-gnomad","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-gnomad/lists"}