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About

Chromoscope is developed and maintained by the members of Department of Biomedical Informatics at Harvard Medical School.

Team​

  • Sehi L'Yi (HiDIVE Lab)
  • Dominika Maziec (Park Lab)
  • Victoria Stevens (Park Lab)
  • Trevor Manz (HiDIVE Lab)
  • Alexander Veit (Park Lab)
  • Michele Berselli (Park Lab)
  • Peter J Park (Park Lab)
  • Dominik Glodzik (Park Lab)
  • Nils Gehlenborg (HiDIVE Lab)

Citation​

When citing Chromoscope in your paper, please cite the following publication.

L'Yi et al. Chromoscope: Interactive Multiscale Visualization for Structural Variation in Human Genomes. OSF Preprints, 10 May 2023. 10.31219/osf.io/pyqrx

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An URL of the point mutation index file (",(0,r.kt)("inlineCode",{parentName:"td"},".tbi"),").")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"vcf2")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"string")),(0,r.kt)("td",{parentName:"tr",align:null},"Optional. An URL of the the indel file (",(0,r.kt)("inlineCode",{parentName:"td"},".vcf"),").")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"vcf2Index")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"string")),(0,r.kt)("td",{parentName:"tr",align:null},"Optional. An URL of the indel index file (",(0,r.kt)("inlineCode",{parentName:"td"},".tbi"),").")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"bam")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"string")),(0,r.kt)("td",{parentName:"tr",align:null},"Optional. An URL of the BAM file (",(0,r.kt)("inlineCode",{parentName:"td"},".bam"),").")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"bai")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"string")),(0,r.kt)("td",{parentName:"tr",align:null},"Optional. An URL of the BAM index file (",(0,r.kt)("inlineCode",{parentName:"td"},".bai"),").")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"note")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"string")),(0,r.kt)("td",{parentName:"tr",align:null},"Optional. A textual annotation.")))),(0,r.kt)("p",null,"A single-sample example:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-js"},'{\n "id": "7a921087-8e62-4a93-a757-fd8cdbe1eb8f",\n "cancer": "ovarian",\n "assembly": "hg19",\n "sv": "https://s3.amazonaws.com/gosling-lang.org/data/SV/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.pcawg_consensus_1.6.161022.somatic.sv.bedpe",\n "cnv": "https://s3.amazonaws.com/gosling-lang.org/data/SV/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.consensus.20170119.somatic.cna.annotated.txt"\n}\n')),(0,r.kt)("p",null,"A multi-sample example:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-js"},'[\n {\n "id": "SRR7890905",\n "cancer": "breast",\n "assembly": "hg38",\n "drivers": "https://gist.githubusercontent.com/sehilyi/350b9e633c52ad97df00a0fc13a8839a/raw/c47b9ba33f1c9e187c69d1dadd01838db44d3b29/driver.txt",\n "sv": "https://somatic-browser-test.s3.amazonaws.com/SVTYPE_SV_test_tumor_normal_with_panel.bedpe",\n "cnv": 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