{
  "assemblies": [
    {
      "name": "hg38",
      "aliases": ["GRCh38"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "hg38-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
        }
      }
    },
    {
      "name": "der3_RARB_BICC1_TRHDE",
      "displayName": "COLO829 derivative allele (RARB/BICC1/TRHDE)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "der3_RARB_BICC1_TRHDE-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "uri": "der3_RARB.derivative.fa.gz"
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ncbi_refseq_hg38",
      "name": "NCBI RefSeq genes",
      "assemblyNames": ["hg38"],
      "category": ["Annotation"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "indexType": "CSI",
          "location": {
            "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz.csi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "COLO829_somatic_sv",
      "name": "COLO829 somatic SVs (nanomonsv)",
      "assemblyNames": ["hg38"],
      "category": ["COLO829 (melanoma, ONT R10)"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "COLO829.somatic-sv.vcf.gz"
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "COLO829_tumor_ont",
      "name": "COLO829 tumour (ONT R10, haplotagged)",
      "assemblyNames": ["hg38"],
      "category": ["COLO829 (melanoma, ONT R10)"],
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "https://ont-open-data.s3.amazonaws.com/colo829_2024.03/wf_somatic_variation/sup/COLO829_tumor.ht.cram"
        },
        "craiLocation": {
          "uri": "https://ont-open-data.s3.amazonaws.com/colo829_2024.03/wf_somatic_variation/sup/COLO829_tumor.ht.cram.crai"
        }
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "COLO829BL_normal_ont",
      "name": "COLO829BL matched normal (ONT R10)",
      "assemblyNames": ["hg38"],
      "category": ["COLO829 (melanoma, ONT R10)"],
      "adapter": {
        "type": "BamAdapter",
        "uri": "https://ont-open-data.s3.amazonaws.com/colo829_2024.03/basecalls/colo829bl/sup/PAU59807.d052sup4305mCG_5hmCGvHg38.bam"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "COLO829_tumor_coverage",
      "name": "COLO829 tumour coverage (50 kb bins)",
      "assemblyNames": ["hg38"],
      "category": ["COLO829 (melanoma, ONT R10)"],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "COLO829_tumor.coverage.bw"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "COLO829_normal_coverage",
      "name": "COLO829BL normal coverage (50 kb bins)",
      "assemblyNames": ["hg38"],
      "category": ["COLO829 (melanoma, ONT R10)"],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "COLO829_normal.coverage.bw"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "der3_vs_hg38",
      "name": "Derivative allele vs hg38",
      "assemblyNames": ["der3_RARB_BICC1_TRHDE", "hg38"],
      "category": ["COLO829 (melanoma, ONT R10)"],
      "adapter": {
        "type": "PairwiseIndexedPAFAdapter",
        "assemblyNames": ["der3_RARB_BICC1_TRHDE", "hg38"],
        "pifGzLocation": {
          "uri": "der3_RARB.vs_reference.pif.gz"
        },
        "index": {
          "indexType": "TBI",
          "location": {
            "uri": "der3_RARB.vs_reference.pif.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "der3_segments",
      "name": "Where each segment came from",
      "assemblyNames": ["der3_RARB_BICC1_TRHDE"],
      "category": ["COLO829 (melanoma, ONT R10)"],
      "adapter": {
        "type": "BedTabixAdapter",
        "bedGzLocation": {
          "uri": "der3_RARB.derivative_segments.bed.gz"
        },
        "index": {
          "location": {
            "uri": "der3_RARB.derivative_segments.bed.gz.tbi"
          }
        }
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "reads_vs_der3",
      "name": "Spanning reads realigned to the derivative",
      "assemblyNames": ["der3_RARB_BICC1_TRHDE"],
      "category": ["COLO829 (melanoma, ONT R10)"],
      "adapter": {
        "type": "BamAdapter",
        "uri": "der3_RARB.reads_vs_derivative.bam"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "K562_star_fusion",
      "name": "K562 STAR-Fusion calls (DepMap 24Q4)",
      "assemblyNames": ["hg38"],
      "category": ["K562 (CML)"],
      "adapter": {
        "type": "StarFusionAdapter",
        "starFusionLocation": {
          "uri": "K562.star-fusion.tsv"
        }
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "K562_isoseq",
      "name": "K562 PacBio Iso-Seq (ENCODE)",
      "assemblyNames": ["hg38"],
      "category": ["K562 (CML)"],
      "adapter": {
        "type": "BamAdapter",
        "uri": "K562_isoseq.bam"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "K562_cn",
      "name": "K562 copy-number segments (DepMap WGS)",
      "assemblyNames": ["hg38"],
      "category": ["K562 (CML)"],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "K562_cn.bw"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "K562_10x_sv",
      "name": "K562 DNA breakpoints (10X linked reads, lifted to hg38)",
      "assemblyNames": ["hg38"],
      "category": ["K562 (CML)"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "K562.10x-large-sv.vcf.gz"
        },
        "index": {
          "location": {
            "uri": "K562.10x-large-sv.vcf.gz.tbi"
          }
        }
      }
    }
  ],
  "defaultSession": {
    "name": "COLO829 multi-hop rearrangement",
    "views": [
      {
        "type": "LinearGenomeView",
        "init": {
          "assembly": "hg38",
          "loc": "chr3:25,320,000-25,370,000",
          "tracks": [
            "ncbi_refseq_hg38",
            "COLO829_somatic_sv",
            "COLO829_tumor_ont"
          ]
        }
      }
    ]
  }
}