IGV browser settings

Default tracks

The default file formats for viewing alignments in Scout is BAM or CRAM. Scout utilizes the embeddable interactive genome visualization tool igv.js to display sample tracks and the following default tracks, available in the IGV browser by default for both genome builds GRCh37 (hg19) and GRCh38 (hg38):

Reference genome track
Genes track
ClinVar SNVs track
ClinVar CNVs track

Reference genome and genes track are collected from the Broad Institute Amazon S3 storage, while the ClinVar tracks are available in the UCSC Genomics Institute Sequence and Annotation Downloads

Custom tracks

One or more custom tracks could be additionally loaded and visualized in the Scout IGV browser by including them in the general Scout configuration file. To add a public track of type "variant" to Scout use the following example line:

CLOUD_IGV_TRACKS = [
    {
        "name": "custom_public_bucket",
        "access": "public",
        "tracks": [
            {
                "name": "Display name of track",
                "type": "variant",
                "format": "vcf",
                "build": "37", # or "38"
                "url": "url_to_resource",
                "indexURL": "url_to_resource_index",
            }
        ],
    },
]