From 88b79f2be6ee04c879208593e1a45cd778e77c9f Mon Sep 17 00:00:00 2001 From: SEHI L'YI Date: Thu, 16 Jan 2025 20:18:25 -0500 Subject: [PATCH] Update of through-data-config.md --- docs/docs/loading-data/through-data-config.md | 230 +++++++++--------- 1 file changed, 115 insertions(+), 115 deletions(-) diff --git a/docs/docs/loading-data/through-data-config.md b/docs/docs/loading-data/through-data-config.md index 142fe9fa..70f9f903 100644 --- 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 + } ] - } } -] +} ```