Data Configuration

You can load a large number of samples through data configurations. You need to (1) make a data config file (.json) that contains the information for individual samples, (2) store the config file in a HTTPS file server (e.g., AWS S3 or GitHub Gist), and (3) use it with the external parameter of the Chromoscope URL:

// format
https://chromoscope.bio/app/?external=[URL_TO_YOUR_CONFIG_FILE]

// example
https://chromoscope.bio/app/?external=https://gist.githubusercontent.com/sehilyi/a9bbbc3e63806d2282e1959e27a65a53/raw/b6c0ab07a220027196746f46607e916bd9751c70/goscan-multiple-samples.json

For each sample, you need to prepare the following information in a JSON object.

Property	Type	Note
id	string	Required. Unique ID.
cancer	string	Required. Type of a cancer.
assembly	'hg38' or 'hg19'	Required. Assembly.
sv	string	Required. An URL of the SV bedpe file (.bedpe).
cnv	string	Optional. An URL of the CNV text file (.tsv).
drivers	string	Optional. An URL of a file that contains drivers (.tsv or .json).
vcf	string	Optional. An URL of the point mutation file (.vcf).
vcfIndex	string	Optional. An URL of the point mutation index file (.tbi).
vcf2	string	Optional. An URL of the the indel file (.vcf).
vcf2Index	string	Optional. An URL of the indel index file (.tbi).
bam	string	Optional. An URL of the BAM file (.bam).
bai	string	Optional. An URL of the BAM index file (.bai).
note	string	Optional. A textual annotation.

A single-sample example:

{
    "id": "7a921087-8e62-4a93-a757-fd8cdbe1eb8f",
    "cancer": "ovarian",
    "assembly": "hg19",
    "sv": "https://s3.amazonaws.com/gosling-lang.org/data/SV/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.pcawg_consensus_1.6.161022.somatic.sv.bedpe",
    "cnv": "https://s3.amazonaws.com/gosling-lang.org/data/SV/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.consensus.20170119.somatic.cna.annotated.txt"
}

A multi-sample example:

[
    {
        "id": "SRR7890905",
        "cancer": "breast",
        "assembly": "hg38",
        "drivers": "https://gist.githubusercontent.com/sehilyi/350b9e633c52ad97df00a0fc13a8839a/raw/c47b9ba33f1c9e187c69d1dadd01838db44d3b29/driver.txt",
        "sv": "https://somatic-browser-test.s3.amazonaws.com/SVTYPE_SV_test_tumor_normal_with_panel.bedpe",
        "cnv": "https://gist.githubusercontent.com/sehilyi/6fbceae35756b13472332d6b81b10803/raw/596428a8b0ebc00e7f8cbc52b050db0fbd6e19a5/SRR7890943.ascat.v3.cnv.tsv",
        "bam": "https://somatic-browser-test.s3.amazonaws.com/SRR7890905_GAPFI2USVS21.bam",
        "bai": "https://somatic-browser-test.s3.amazonaws.com/SRR7890905_GAPFI2USVS21.bam.bai",
        "note": "This is a test note"
    },
    {
        "id": "bc0dee07-de20-44d6-be65-05af7e63ac96",
        "cancer": "gastric",
        "assembly": "hg19",
        "sv": "https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/bc0dee07-de20-44d6-be65-05af7e63ac96.pcawg_consensus_1.6.161116.somatic.sv.bedpe",
        "cnv": "https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/bc0dee07-de20-44d6-be65-05af7e63ac96.consensus.20170119.somatic.cna.txt",
        "vcf": "https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/bc0dee07-de20-44d6-be65-05af7e63ac96.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz",
        "vcfIndex": "https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/bc0dee07-de20-44d6-be65-05af7e63ac96.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi",
        "vcf2": "https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/bc0dee07-de20-44d6-be65-05af7e63ac96.consensus.20161006.somatic.indel.sorted.vcf.gz",
        "vcf2Index": "https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/bc0dee07-de20-44d6-be65-05af7e63ac96.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi",
        "note": "This is a test note"
    }
]