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samples.ts
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import { Assembly } from 'gosling.js/dist/src/gosling-schema';
import _7a921087 from '../script/img/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.jpeg';
import _84ca6ab0 from '../script/img/84ca6ab0-9edc-4636-9d27-55cdba334d7d.jpeg';
import _7d332cb1 from '../script/img/7d332cb1-ba25-47e4-8bf8-d25e14f40d59.jpeg';
import _9ae0744a from '../script/img/9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa.jpeg';
import _b27d75ba from '../script/img/b27d75ba-5989-4200-bfe9-f1b7d7cf8008.jpeg';
import _fc8edf46 from '../script/img/fc8edf46-2005-1af4-e040-11ac0d481414.jpeg';
import SRR7890905 from '../script/img/SRR7890905.jpg';
import SRR7890905_Hartwig from '../script/img/SRR7890905_Hartwig.jpg';
import _bc0dee07 from '../script/img/GACA-CN-bc0dee07-de20-44d6-be65-05af7e63ac96.jpeg';
import _f1504811 from '../script/img/OV-AU-f1504811-8363-41e6-b43c-62452b1262d3.jpeg';
import _89dad92e from '../script/img/OV-AU-89dad92e-5b3f-479a-a6da-a94ee7df7f8a.jpeg';
import _b243adb4 from '../script/img/OV-US-b243adb4-b3e7-4e0e-bc0d-625aa8dbb1be.jpeg';
import _84ca6ab0_OV from '../script/img/OV-US-84ca6ab0-9edc-4636-9d27-55cdba334d7d.jpeg';
import _0bfd1043 from '../script/img/OV-US-0bfd1043-816e-e3e4-e050-11ac0c4860c5.jpeg';
export type SampleType = {
group: 'default' | 'doga' | 'vcf';
id: string; // "aliquot ID"
cancer: string; // cancer type
assembly: Assembly; // hg19 or 38
sv: string; // URL of bedpe
cnv?: string; // URL of txt
drivers?: { [k: string]: string | number }[] | string;
bam?: string;
bai?: string;
vcf?: string;
vcfIndex?: string;
vcf2?: string;
vcf2Index?: string;
cnFields?: [string, string, string];
thumbnail?: string;
note?: string;
};
// const samples: SampleType[] = (pcawg as SampleType[]).map(d => { return { group: 'default', ...d }});
// console.log(samples);
const samples: SampleType[] = [
{
group: 'default',
id: 'SRR7890905',
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/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: 'CNV profile - ASCAT. SVs - Sentieon. Mutations and indels - Sentieon',
thumbnail: SRR7890905
},
{
group: 'default',
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',
thumbnail: SRR7890905_Hartwig
},
{
group: 'default',
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',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
// drivers: 'https://gist.githubusercontent.com/sehilyi/01096d32326da8e7f9acc48dd9790332/raw/4f2bbd96ce3d2b6637bd733674f60e197e4d4da9/json-driver.json', // json example
thumbnail: _7a921087
},
{
group: 'default',
id: '7d332cb1-ba25-47e4-8bf8-d25e14f40d59',
cancer: 'sarcoma',
assembly: 'hg19',
sv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/7d332cb1-ba25-47e4-8bf8-d25e14f40d59.pcawg_consensus_1.6.161022.somatic.sv.bedpe',
cnv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/7d332cb1-ba25-47e4-8bf8-d25e14f40d59.consensus.20170119.somatic.cna.annotated.txt',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/7d332cb1-ba25-47e4-8bf8-d25e14f40d59.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/7d332cb1-ba25-47e4-8bf8-d25e14f40d59.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/7d332cb1-ba25-47e4-8bf8-d25e14f40d59.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/7d332cb1-ba25-47e4-8bf8-d25e14f40d59.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
thumbnail: _7d332cb1
},
{
group: 'default',
id: '9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa',
cancer: 'kidney',
assembly: 'hg19',
sv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa.pcawg_consensus_1.6.161022.somatic.sv.bedpe',
cnv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa.consensus.20170119.somatic.cna.annotated.txt',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
thumbnail: _9ae0744a
},
{
group: 'default',
id: 'b27d75ba-5989-4200-bfe9-f1b7d7cf8008',
cancer: 'breast',
assembly: 'hg19',
sv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/b27d75ba-5989-4200-bfe9-f1b7d7cf8008.pcawg_consensus_1.6.161022.somatic.sv.bedpe',
cnv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/b27d75ba-5989-4200-bfe9-f1b7d7cf8008.consensus.20170119.somatic.cna.annotated.txt',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/b27d75ba-5989-4200-bfe9-f1b7d7cf8008.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/b27d75ba-5989-4200-bfe9-f1b7d7cf8008.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/b27d75ba-5989-4200-bfe9-f1b7d7cf8008.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/b27d75ba-5989-4200-bfe9-f1b7d7cf8008.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
thumbnail: _b27d75ba
},
{
group: 'default',
id: 'fc8edf46-2005-1af4-e040-11ac0d481414',
cancer: 'breast',
assembly: 'hg19',
sv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/fc8edf46-2005-1af4-e040-11ac0d481414.pcawg_consensus_1.6.161022.somatic.sv.bedpe',
cnv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/fc8edf46-2005-1af4-e040-11ac0d481414.consensus.20170119.somatic.cna.annotated.txt',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/fc8edf46-2005-1af4-e040-11ac0d481414.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/fc8edf46-2005-1af4-e040-11ac0d481414.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/browserExamples/fc8edf46-2005-1af4-e040-11ac0d481414.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/browserExamples/fc8edf46-2005-1af4-e040-11ac0d481414.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
thumbnail: _fc8edf46
},
// {
// group: 'default',
// id: 'SRR7890905',
// cancer: 'breast',
// assembly: 'hg38',
// 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',
// thumbnail: _SRR7890905
// },
{
group: 'default',
id: 'bc0dee07-de20-44d6-be65-05af7e63ac96', // GACA-CN-
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',
thumbnail: _bc0dee07
},
{
group: 'default',
id: 'f1504811-8363-41e6-b43c-62452b1262d3', // OV-AU-
cancer: 'ovarian',
assembly: 'hg19',
sv: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/f1504811-8363-41e6-b43c-62452b1262d3.pcawg_consensus_1.6.161116.somatic.sv.bedpe',
cnv: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/f1504811-8363-41e6-b43c-62452b1262d3.consensus.20170119.somatic.cna.txt',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/f1504811-8363-41e6-b43c-62452b1262d3.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/f1504811-8363-41e6-b43c-62452b1262d3.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/f1504811-8363-41e6-b43c-62452b1262d3.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/f1504811-8363-41e6-b43c-62452b1262d3.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
thumbnail: _f1504811
},
{
group: 'default',
id: '89dad92e-5b3f-479a-a6da-a94ee7df7f8a', // OV-AU-
cancer: 'ovarian',
assembly: 'hg19',
sv: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/89dad92e-5b3f-479a-a6da-a94ee7df7f8a.pcawg_consensus_1.6.161116.somatic.sv.bedpe',
cnv: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/89dad92e-5b3f-479a-a6da-a94ee7df7f8a.consensus.20170119.somatic.cna.txt',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/89dad92e-5b3f-479a-a6da-a94ee7df7f8a.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/89dad92e-5b3f-479a-a6da-a94ee7df7f8a.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/89dad92e-5b3f-479a-a6da-a94ee7df7f8a.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/89dad92e-5b3f-479a-a6da-a94ee7df7f8a.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
thumbnail: _89dad92e
},
{
group: 'default',
id: 'b243adb4-b3e7-4e0e-bc0d-625aa8dbb1be', // OV-US-
cancer: 'ovarian serous cystadenocarcinoma',
assembly: 'hg19',
sv: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/b243adb4-b3e7-4e0e-bc0d-625aa8dbb1be.pcawg_consensus_1.6.161116.somatic.sv.bedpe',
cnv: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/b243adb4-b3e7-4e0e-bc0d-625aa8dbb1be.consensus.20170119.somatic.cna.txt',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/b243adb4-b3e7-4e0e-bc0d-625aa8dbb1be.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/b243adb4-b3e7-4e0e-bc0d-625aa8dbb1be.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/b243adb4-b3e7-4e0e-bc0d-625aa8dbb1be.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/b243adb4-b3e7-4e0e-bc0d-625aa8dbb1be.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
thumbnail: _b243adb4
},
{
group: 'default',
id: '84ca6ab0-9edc-4636-9d27-55cdba334d7d',
cancer: 'ovarian',
assembly: 'hg19',
sv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/84ca6ab0-9edc-4636-9d27-55cdba334d7d.pcawg_consensus_1.6.161022.somatic.sv.bedpe',
cnv: 'https://s3.amazonaws.com/gosling-lang.org/data/SV/84ca6ab0-9edc-4636-9d27-55cdba334d7d.consensus.20170119.somatic.cna.annotated.txt',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/84ca6ab0-9edc-4636-9d27-55cdba334d7d.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/84ca6ab0-9edc-4636-9d27-55cdba334d7d.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/84ca6ab0-9edc-4636-9d27-55cdba334d7d.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/84ca6ab0-9edc-4636-9d27-55cdba334d7d.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
thumbnail: _84ca6ab0
},
{
group: 'default',
id: '0bfd1043-816e-e3e4-e050-11ac0c4860c5', // OV-US-
cancer: 'prostate adenocarcinoma',
assembly: 'hg19',
sv: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/0bfd1043-816e-e3e4-e050-11ac0c4860c5.pcawg_consensus_1.6.161116.somatic.sv.bedpe',
cnv: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/0bfd1043-816e-e3e4-e050-11ac0c4860c5.consensus.20170119.somatic.cna.txt',
vcf: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/0bfd1043-816e-e3e4-e050-11ac0c4860c5.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz',
vcfIndex:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/0bfd1043-816e-e3e4-e050-11ac0c4860c5.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz.tbi',
vcf2: 'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/0bfd1043-816e-e3e4-e050-11ac0c4860c5.consensus.20161006.somatic.indel.sorted.vcf.gz',
vcf2Index:
'https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/0bfd1043-816e-e3e4-e050-11ac0c4860c5.consensus.20161006.somatic.indel.sorted.vcf.gz.tbi',
thumbnail: _0bfd1043
}
];
export default samples;