Update of through-data-config.md

hms-dbmi · Jan 17, 2025 · 88b79f2 · 88b79f2
1 parent 0ee64c0
commit 88b79f2
Showing 1 changed file with 115 additions and 115 deletions.
diff --git a/docs/docs/loading-data/through-data-config.md b/docs/docs/loading-data/through-data-config.md
@@ -77,137 +77,137 @@ A multi-sample example:
 
 The data for the genome interpretation panel can be recorded as additional features of the configuration file.
 ![Screenshot 2025-01-15 at 10 46 28 AM](https://github.com/user-attachments/assets/02d15e04-0986-4e8e-8da8-2a07eb1119a4)
-For each sample, there is an optional field: `clinicalInfo`, which will display the clinical info if present.
-The `clinicalInfo` has the following fields:
-`summary`, `variants`, `signatures`
+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` | `int` | Required. Chromosomal coordinate of the mutation|
-| `type` | `string` | Optional. Type of variant, eg. bi-allelic, germline, deletion |
-| `cDNA` | `string` | Optional. cDNA coordinate of the mutation, eg. c.524G>A |
-| `protein change` | `string` | Optional. protein consequence of the mutation, eg. p.Arg175His |
-| `VAF` | `float` | Optional. Variant allele fraction of a mutation in the sample, eg. 0.45 |
-| `mutation` | `string` | Optional. Reference and alternative allele in genomic DNA, eg. G>T |
-
-Example of a configuration with the information necessary for the genome interpretation panel
+| `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:
+
 ```js
-[
-    {
-        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",
+{
+    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"
-        }
+        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"
-        }
+            {
+                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
-        }
+            {
+                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
+            }
         ]
-        }
     }
-]
+}
 ```