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IGV browser settings

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, with the exception of old hg19 1kg references, which are served from a Japanese National Institute of Genetics mirror. The ClinVar tracks are available from the UCSC Genomics Institute Sequence and Annotation Downloads

Custom reference tracks

It is possible to add custom reference tracks to the IGV browser in Scout. This is done by adding a CUSTOM_REFERENCE dictionary to the Scout configuration file, with the following structure:

# Custom IGV.js reference tracks: use a local mirror for the most part
CUSTOM_REFERENCE = {
    "37": {
        "id": "hg19",
        "name": "GRCh37 1kg decoy",
        "fastaURL": "/home/proj/production/scout_igv_tracks/seq/grch37_homo_sapiens_-d5-.fasta",
        "indexURL": "/home/proj/production/scout_igv_tracks/seq/grch37_homo_sapiens_-d5-.fasta.fai",
        "cytobandURL": "/home/proj/production/scout_igv_tracks/seq/cytoBand.txt.gz",
        "aliasURL": "https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/data/hg19/hg19_alias.tab",
    },
    "38": {
        "id": "hg38",
        "name": "GRCh38",
        "fastaURL": "/home/proj/production/scout_igv_tracks/seq/grch38_homo_sapiens_-assembly-.fasta",
        "indexURL": "/home/proj/production/scout_igv_tracks/seq/grch38_homo_sapiens_-assembly-.fasta.fai",
        "cytobandURL": "/home/proj/production/scout_igv_tracks/seq/cytoBand.txt.gz",
        "aliasURL": "https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/data/hg38/hg38_alias.tab",
        "chromosomeOrder": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM",
    },
}

It is possible to locally mirror only some of the files, and give URLs for others, but if you do add any CUSTOM_REFERENCE you will need to supply locations for all the keys as the default references will no longer be configured.

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",
            }
        ],
    },
]