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"
}
]
Genome Interpretation Panel
The data for the genome interpretation panel can be recorded as additional features of the configuration file.
For each sample, there is an optional property (
clinicalInfo) to provide clinical information. If present, this information will be displayed in Chromoscope (the panel on the right-most side).
You can provide three fields under the clinicalInfo property: summary, variants, signatures
The summary field is a list of elements with two fields: label and value. Label can be any string, and will be displayed next to value which can also be any string.
The variants field is a list of variants, each with the following fields:
| Property | Type | Note |
|---|---|---|
gene | string | Required. Gene name |
chr | string | Required. Chromosome with the variant, including the chr prefix |
position | number | Required. Chromosomal coordinate of the mutation |
type | string | Optional. Type of variant, e.g., "bi-allelic", "germline", "deletion" |
cDNA | string | Optional. cDNA coordinate of the mutation, e.g., "c.524G>A" |
protein change | string | Optional. protein consequence of the mutation, e.g., "p.Arg175His" |
VAF | number | Optional. Variant allele fraction of a mutation in the sample, e.g., 0.45 |
mutation | string | Optional. Reference and alternative allele in genomic DNA, e.g., "G>T" |
Refer to an example configuration file that contains the clinical information necessary for displaying the genome interpretation panel:
{
id: "SRR7890905_Hartwig",
cancer: "breast",
assembly: "hg38",
vcf: "https://somatic-browser-test.s3.amazonaws.com/SNV_test_tumor_normal_with_panel.vcf.gz",
vcfIndex: "https://somatic-browser-test.s3.amazonaws.com/SNV_test_tumor_normal_with_panel.vcf.gz.tbi",
vcf2: "https://somatic-browser-test.s3.amazonaws.com/INDEL_test_tumor_normal_with_panel.vcf.gz",
vcf2Index: "https://somatic-browser-test.s3.amazonaws.com/INDEL_test_tumor_normal_with_panel.vcf.gz.tbi",
sv: "https://somatic-browser-test.s3.amazonaws.com/SRR7890905/SRR7890905.gripss.filtered.bedpe",
cnv: "https://somatic-browser-test.s3.amazonaws.com/SRR7890905/SRR7890905.purple.cnv.somatic.reformatted.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: "CNV profile - Purple. SVs - Gridss. Mutations and indels - Sentieon",
clinicalInfo: {
summary: [
{
label: "grade",
value: "2"
},
{
label: "age",
value: "32"
},
{
label: "AIMS Subtype",
value: "Basal"
},
{
label: "Treatment",
value: "None"
},
{
label: "Lymph node status",
value: "Negative"
}
],
variants: [
{
gene: "TP53",
type: "biallelic",
cDNA: "c.524G>A",
protein change: "p.Arg175His",
VAF: "0.97",
chr: "chr17",
position: "7677976",
mutation: "C>T"
},
{
gene: "BRCA2",
cDNA: "c.4777G>T",
protein change: "p.Glu1593Ter",
VAF: "0.45",
chr: "chr13",
position: "32357888",
mutation: "G>T"
},
{
gene: "PTEN",
type: "deletion",
chr: "chr10",
position: "87917777"
},
{
gene: "CDKN2A",
type: "deletion",
chr: "chr9",
position: "21981538"
},
{
gene: "MET",
type: "amplification",
chr: "chr7",
position: "116735286"
}
],
signatures: [
{
type: "point_mutations",
count: "5100",
label: "HRD-attributed point mutations",
hrDetect: true
},
{
type: "indels",
count: "500",
label: "HRD-attributed small deletions with micro-homology",
hrDetect: true
},
{
type: "svs_duplications",
count: "120",
label: "HRD-attributed small tandem duplications",
hrDetect: true
},
{
type: "svs_deletions",
count: "50",
label: "HRD-attributed small deletions",
hrDetect: true
},
{
type: "point_mutations",
count: "1000",
label: "APOBEC-attributed small substitutions",
hrDetect: false
}
]
}
}