{
  "assemblies": [
    {
      "name": "GRCh38_GIABv3",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "GRCh38_GIABv3-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "GRCh38_GIABv3.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "GRCh38_GIABv3.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "GRCh38_GIABv3.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      },
      "cytobands": {
        "adapter": {
          "type": "CytobandAdapter",
          "uri": "https://jbrowse.org/ucsc/hg38/hg38.cytoBand.txt.gz"
        }
      }
    },
    {
      "name": "HG008T_v3.2",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG008T_v3.2-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "HG008T_v3.2.fasta.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "HG008T_v3.2.fasta.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "HG008T_v3.2.fasta.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "configuration": {},
  "connections": [],
  "defaultSession": {
    "name": "New Session"
  },
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "grch38_cytobands",
      "name": "Cytobands (UCSC hg38)",
      "assemblyNames": ["GRCh38_GIABv3"],
      "category": ["Reference"],
      "adapter": {
        "type": "BedAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/hg38.cytoBand.txt.gz",
        "columnNames": ["chrom", "chromStart", "chromEnd", "name", "gieStain"]
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "grch38_cytobands-LinearBasicDisplay",
          "color": "jexl:{gneg:'rgb(227,227,227)',gpos25:'rgb(142,142,142)',gpos50:'rgb(85,85,85)',gpos75:'rgb(57,57,57)',gpos100:'rgb(0,0,0)',gvar:'rgb(0,0,0)',stalk:'rgb(127,127,127)',acen:'#800'}[get(feature,'gieStain')] || 'black'",
          "height": 50
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "hg008t_benchmark_sv",
      "name": "HG008-T V0.5 draft benchmark somatic SVs",
      "category": ["Variant calls"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg008t_somatic_cnv",
      "name": "HG008-T somatic CNV",
      "category": ["Variant calls"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "BedAdapter",
        "bedLocation": {
          "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/GRCh38_HG008-T-V0.5_somatic-CNV_PASS.draftbenchmark.calls.bed",
          "locationType": "UriLocation"
        },
        "columnNames": [
          "chrom",
          "start",
          "end",
          "total_copy_number",
          "hap1_copy_number",
          "hap2_copy_number",
          "name"
        ]
      },
      "displayDefaults": {
        "labels": {
          "name": "jexl:'CN '+get(feature,'total_copy_number')+' ('+get(feature,'hap1_copy_number')+'|'+get(feature,'hap2_copy_number')+')'"
        },
        "color": {
          "field": "total_copy_number",
          "scale": "threshold",
          "domain": ["1", "2", "3", "4"],
          "range": ["#2166ac", "#92c5de", "#e0e0e0", "#f4a582", "#b2182b"],
          "labels": ["CN 0", "CN 1", "CN 2", "CN 3", "CN 4+"],
          "title": "Copy number"
        }
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "HG008-N-P_PacBio-HiFi-Revio_20240125_35x_GRCh38-GIABv3.cram.all",
      "name": "HG008-N matched normal coverage",
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "HG008-N-P_PacBio-HiFi-Revio_20240125_35x_GRCh38-GIABv3.cram.all.bw",
          "locationType": "UriLocation"
        }
      },
      "category": ["Coverage"],
      "assemblyNames": ["GRCh38_GIABv3"]
    },
    {
      "type": "SyntenyTrack",
      "trackId": "HG008T_v3.2_pif",
      "name": "HG008T v3.2",
      "assemblyNames": ["HG008T_v3.2", "GRCh38_GIABv3"],
      "adapter": {
        "type": "PairwiseIndexedPAFAdapter",
        "assemblyNames": ["HG008T_v3.2", "GRCh38_GIABv3"],
        "pifGzLocation": {
          "uri": "HG008T_v3.2.pif.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "indexType": "TBI",
          "location": {
            "uri": "HG008T_v3.2.pif.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "HG008-N-P_PacBio-HiFi-Revio_20240125_35x_GRCh38-GIABv3",
      "name": "HG008-N-P_PacBio-HiFi-Revio_20240125_35x_GRCh38-GIABv3",
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/PacBio_Revio_20240125/HG008-N-P_PacBio-HiFi-Revio_20240125_35x_GRCh38-GIABv3.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/PacBio_Revio_20240125/HG008-N-P_PacBio-HiFi-Revio_20240125_35x_GRCh38-GIABv3.bam.bai",
            "locationType": "UriLocation"
          },
          "indexType": "BAI"
        }
      },
      "category": ["Reads"],
      "assemblyNames": ["GRCh38_GIABv3"]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
      "name": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "https://jbrowse.org/demos/cgiab/HG008-T_PacBio-HiFi-Revio_116x.demo_slices.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/cgiab/HG008-T_PacBio-HiFi-Revio_116x.demo_slices.bam.bai",
            "locationType": "UriLocation"
          },
          "indexType": "BAI"
        }
      },
      "category": ["Reads"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "description": "Rehosted slice of the 118 GB NIST HG008-T PacBio HiFi Revio BAM, covering only the three windows the C-GIAB figures use: chr3:139,966,414-139,986,414 and chr13:114,343,244-114,363,244 (the SV_20 translocation) and chr9:21,920,000-22,000,000 (CDKN2A). Elsewhere the track is empty. Source: ftp-trace.ncbi.nlm.nih.gov ReferenceSamples/giab/data_somatic/HG008"
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "HG008_log2ratio",
      "name": "HG008 log2(tumor/normal) coverage ratio",
      "category": ["CNV"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "HG008_log2ratio.bw",
          "locationType": "UriLocation"
        }
      },
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "HG008_log2ratio-LinearWiggleDisplay",
          "mark": "point",
          "summaryScoreMode": "mean",
          "size": 1,
          "scales": { "y": { "domainMin": -2, "domainMax": 2 } },
          "height": 120
        }
      ]
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "HG008-T_bicseq2",
      "name": "HG008-T copy ratio, segmented (NYGC BIC-seq2, log2 T/N)",
      "category": ["CNV"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "BedGraphAdapter",
        "bedGraphLocation": {
          "uri": "HG008-T_bicseq2_log2ratio.bedgraph",
          "locationType": "UriLocation"
        }
      },
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "HG008-T_bicseq2-LinearWiggleDisplay",
          "mark": "line",
          "color": "#0068d1",
          "scales": {
            "y": { "domainMin": -2, "domainMax": 1.5, "grid": true }
          },
          "height": 90
        }
      ]
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "HG008-T_baf",
      "name": "HG008-T B-allele frequency (BAF)",
      "category": ["CNV"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "HG008-T_baf.bcftools.bw",
          "locationType": "UriLocation"
        },
        "resolutionMultiplier": 0.001
      },
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "HG008-T_baf-LinearWiggleDisplay",
          "mark": "point",
          "size": 1,
          "scales": { "y": { "domainMin": 0, "domainMax": 1 } },
          "height": 120
        }
      ]
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "HG008-T_coverage_perbase",
      "name": "HG008-T fine-scale coverage (per-base, CDKN2A locus)",
      "category": ["CNV"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "HG008-T_coverage_perbase.bw",
          "locationType": "UriLocation"
        }
      },
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "HG008-T_coverage_perbase-LinearWiggleDisplay",
          "scales": { "y": { "domainMin": 0, "domainMax": 100 } },
          "height": 120
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "HG008-T_wakhan_cnv",
      "name": "HG008-T Wakhan haplotype-specific CNV segments",
      "category": ["Variant calls"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "BedAdapter",
        "bedLocation": {
          "uri": "HG008-T_wakhan_cnv.bed",
          "locationType": "UriLocation"
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "HG008-T_wakhan_cnv-LinearBasicDisplay",
          "labels": {
            "name": "jexl:'CN '+get(feature,'total_copy_number')+' ('+get(feature,'hap1_copy_number')+'|'+get(feature,'hap2_copy_number')+')'"
          }
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg38_ncbiRefSeq_ucsc",
      "name": "NCBI RefSeq genes (hg38)",
      "category": ["Genes"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg008_subclonal_cnv",
      "name": "HG008-T subclonal CNV (per-clone CNVkit)",
      "category": ["CNV"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "BedTabixAdapter",
        "bedGzLocation": {
          "uri": "HG008T-clones.cnv.multirow.bed.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "indexType": "TBI",
          "location": {
            "uri": "HG008T-clones.cnv.multirow.bed.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearMultiRowFeatureDisplay",
          "displayId": "hg008_subclonal_cnv-LinearMultiRowFeatureDisplay",
          "rows": "clone",
          "color": {
            "field": "cn",
            "scale": "threshold",
            "domain": ["1", "2", "3", "4"],
            "range": ["#2166ac", "#92c5de", "#e0e0e0", "#f4a582", "#b2182b"],
            "labels": [
              "CNVkit CN 0",
              "CNVkit CN 1",
              "CNVkit CN 2",
              "CNVkit CN 3",
              "CNVkit CN 4+"
            ],
            "title": "Copy number"
          }
        }
      ],
      "description": "Per-clone CNVkit integer copy number for eight HG008-T single-cell-derived clonal lines. CNVkit centers log2 on each sample's own median, so these integers are relative to the clone's modal state, not absolute: HG008-T is hypodiploid, so its balanced regions land on CN 3 here rather than CN 2. Read them against the benchmark CNV track, whose total_copy_number is absolute."
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg008_wakhan_haplotype",
      "name": "HG008-T Wakhan copy number per haplotype",
      "category": ["CNV"],
      "assemblyNames": ["GRCh38_GIABv3"],
      "adapter": {
        "type": "BedAdapter",
        "bedLocation": {
          "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_Wakhan-CNA_20240308/bed_output/HG008_HiFi_copynumbers_segments.bed",
          "locationType": "UriLocation"
        }
      },
      "displays": [
        {
          "type": "LinearMultiRowFeatureDisplay",
          "displayId": "hg008_wakhan_haplotype-LinearMultiRowFeatureDisplay",
          "rows": "haplotype",
          "color": {
            "field": "copynumber_state",
            "scale": "threshold",
            "domain": ["0.5", "1.5"],
            "range": ["#2166ac", "#bdbdbd", "#f4a582"],
            "labels": ["Haplotype lost (0)", "One copy", "Two or more copies"],
            "title": "Copy number per haplotype"
          }
        }
      ]
    }
  ]
}