https://tgg-viewer.broadinstitute.org

The Translational Genomics Group (TGG) Viewer is a free, open-source web app for visualizing splice junctions, expression, and other sequencing data genome-wide using IGV.js

Features:

• Supports these file formats: .bigWig, .junctions.bed.gz, .vcf, .bam, .cram.
• Includes reference tracks from GTEx v8 muscle, blood, and fibroblast samples.
• Lets you display data files or reference tracks from any Google bucket to which you have read-access.
• Retrieves just the on-screen sections of the files directly from Google buckets.
• Allows gene or locus lists to be added to side bars for quick navigation across a list of regions.

Settings File Format:

``` { "genome": "hg38", // "hg19" or "hg38" "locus": "chr15:92,835,700-93,031,800", // initial IGV.js locus
"bamOptions": { // IGV.js bam track options "trackHeight": 200, "viewAsPairs": false, "showSoftClips": true, "alignmentShading": "strand" }, "sjOptions": { // IGV.js splice junctions track options "trackHeight": 170, "colorBy": "strand", "colorByNumReadsThreshold": 5, "thicknessBasedOn": "numUniqueReads", "bounceHeightBasedOn": "random", "labelWith": "uniqueReadCount", "showOnlyPlusStrand": false, "showOnlyMinusStrand": false, "hideAnnotated": false, "hideUnannotated": false, "minUniquelyMappedReads": 0, "minTotalReads": 1, "maxFractionMultiMappedReads": 1, "minSplicedAlignmentOverhang": 0 }, "vcfOptions": { // IGV.js vcf track options "displayMode": "EXPANDED" }, "selectedRowNamesByCategoryName": { 0: [], 1: [] }, "rowsInCategories": [ { "categoryName": "Reference Data", "rows": [ { "name": "row1", "data": [ { "url": "gs://../file.bam", "type": "alignment", "label": "l" }, // * "type" and "label" are optional { "url": "gs://../file2.bed", "type": "bed", "label": "l2" }, ], } ] }, { "categoryName": "gCNV Batches", "rows": [ { "name": "gCNV batch1" "data": [ { "type": "gCNV_bed", "url": "gs://../file2.bed", "samples": [ "sample1", "sample2", "sample3",...]}, ], }, { "name": "sample1" "data": [ { "type": "vcf", "url": "gs://../file.vcf", "name": "l" }, // * "type" and "label" are optional { "type": "alignment", "url": "gs://../file.vcf", "name": "l" }, // * "type" and "label" are optional

                ]
            },
        ]
    }
]

} ```