- config:
    default_annotation:
    - name: cadd_raw
      nucleotide_aggregator: max
      position_aggregator: max
      source: cadd_raw
    - name: cadd_phred
      nucleotide_aggregator: max
      position_aggregator: max
      source: cadd_phred
    scores:
    - desc: ''
      id: cadd_raw
      index: 4
      type: float
    - desc: ''
      id: cadd_phred
      index: 5
      type: float
    table:
      alternative:
        index: 3
      chrom:
        index: 0
      filename: CADD.bedgraph.gz
      format: tabix
      header_mode: none
      pos_begin:
        index: 1
      reference:
        index: 2
    type: np_score
  id: hg19/CADD
  manifest:
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    name: CADD.bedgraph.gz
    size: 18459035
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    name: CADD.bedgraph.gz.tbi
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    name: genomic_resource.yaml
    size: 592
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    name: index.html
    size: 2182
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    size: 18985
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    name: statistics/stats_hash
    size: 876
  version: '0'
- config:
    filename: refGene201309.txt
    format: default
    meta:
      description: '## refGene gene models from 2013-09


        Old gene models used by GPF up to 2019-02.

        '
      labels: null
    type: gene_models
  id: hg19/GATK_ResourceBundle_5777_b37_phiX174_short/gene_models/refGene_201309
  manifest:
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    name: statistics/stats.yaml
    size: 615
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    name: statistics/stats_hash
    size: 127
  version: '0'
- config:
    PARS:
      X:
      - X:60001-2699520
      - X:154931044-155260560
      Y:
      - Y:10001-2649520
      - Y:59034050-59363566
    chrom_prefix: ''
    filename: chrAll.fa
    meta:
      description: '## HG19 Reference Genome Fragment


        Default HG19 reference genome used by GPF

        '
      labels: null
    type: genome
  id: hg19/GATK_ResourceBundle_5777_b37_phiX174_short/genome
  manifest:
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    size: 915148
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    name: genomic_resource.yaml
    size: 302
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    size: 3104
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    name: statistics/1_statistic.yaml
    size: 389
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    name: statistics/2_statistic.yaml
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    name: statistics/X_statistic.yaml
    size: 382
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    size: 820
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  version: '0'
- config:
    default_annotation:
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      nucleotide_aggregator: max
      position_aggregator: max
      source: MPC
    scores:
    - desc: ''
      histogram:
        number_of_bins: 100
        type: number
        view_range:
          max: 5.0
          min: 0.0
        y_log_scale: true
      id: MPC
      name: MPC
      type: float
    table:
      alternative:
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      chrom:
        name: chrom
      filename: fordist_constraint_official_mpc_values_v2.txt.gz
      format: tabix
      pos_begin:
        name: pos
      reference:
        name: ref
    type: np_score
  id: hg19/MPC
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    size: 137
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    size: 1907
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  version: '0'
- config:
    default_annotation:
    - name: score0
      position_aggregator: max
      source: score0
    - name: score2
      position_aggregator: max
      source: score2
    - name: score4
      position_aggregator: max
      source: score4
    scores:
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      name: score0
      type: float
    - id: score2
      name: score2
      type: float
    - id: score4
      name: score4
      type: float
    table:
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      filename: scores1.tsv.gz
      format: tabix
      pos_begin:
        name: POS
      pos_end:
        name: POS
    type: position_score
  id: hg19/internal/scores1
  manifest:
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    size: 572
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  version: '0'
- config:
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      position_aggregator: max
      source: score0_incomplete_cov
    scores:
    - id: score0_incomplete_cov
      name: score0
      type: float
    table:
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      filename: scores_incomplete_coverage.tsv.gz
      format: tabix
      pos_begin:
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      pos_end:
        name: POS
    type: position_score
  id: hg19/internal/scores_incomplete_coverage
  manifest:
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    size: 405
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  version: '0'
- config:
    default_annotation:
    - dest: phastCons100
      position_aggregator: max
      source: phastCons100
    scores:
    - desc: phastCons100
      histogram:
        number_of_bins: 10
        type: number
        view_range:
          max: 1.0
          min: 0.0
      id: phastCons100
      index: 3
      type: float
    table:
      chrom:
        index: 0
      filename: phastCons100.bedGraph.gz
      format: tabix
      header_mode: none
      pos_begin:
        index: 1
      pos_end:
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    type: position_score
  id: hg19/phastCons100
  manifest:
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    name: genomic_resource.yaml
    size: 516
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    name: index.html
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  version: '0'
- config:
    filename: refSeq_20200330.txt
    format: refseq
    meta:
      description: '## refSeq gene models for HG38 from 2020-03


        Default gene models used by GPF for HG38.

        '
      labels: null
    type: gene_models
  id: hg38/GRCh38-hg38/gene_models/refSeq_20200330
  manifest:
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    name: genomic_resource.yaml
    size: 200
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    name: statistics/stats.yaml
    size: 474
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    name: statistics/stats_hash
    size: 128
  version: '0'
- config:
    PARS:
      X:
      - chrX:10000-2781479
      - chrX:155701382-156030895
      Y:
      - chrY:10000-2781479
      - chrY:56887902-57217415
    chrom_prefix: ''
    filename: GRCh38_full_analysis_set_plus_decoy_hla.fa
    meta:
      description: "## HG38 Reference Genome \n\nDefault HG38 reference genome used\
        \ by GPF\n"
      labels: null
    type: genome
  id: hg38/GRCh38-hg38/genome
  manifest:
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    size: 2840225
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    name: genomic_resource.yaml
    size: 339
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    name: index.html
    size: 3169
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    size: 401
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    size: 401
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    size: 771
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  version: '0'
- config:
    default_annotation:
    - name: cadd_raw
      nucleotide_aggregator: max
      position_aggregator: max
      source: cadd_raw
    - name: cadd_phred
      nucleotide_aggregator: max
      position_aggregator: max
      source: cadd_phred
    scores:
    - desc: ''
      id: cadd_raw
      name: RawScore
      type: float
    - desc: ''
      id: cadd_phred
      name: PHRED
      type: float
    table:
      alternative:
        name: Alt
      chrom:
        name: Chrom
      filename: TESTCADD.tsv.gz
      format: tabix
      pos_begin:
        name: Pos
      reference:
        name: Ref
    type: np_score
  id: hg38/TESTCADD
  manifest:
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  version: '0'
- config:
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      source: altFreq
    - name: alt_freq2
      source: altFreq2
    scores:
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      id: altFreq
      name: all.altFreq
      type: float
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      id: altFreq2
      name: all.altFreq2
      type: float
    table:
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      chrom:
        name: chr
      filename: TESTFreq.tsv.gz
      format: tabix
      pos_begin:
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      reference:
        name: ref
    type: allele_score
  id: hg38/TESTFreq
  manifest:
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  version: '0'
- config:
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      source: test_score
    scores:
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      position_aggregator: mean
      type: float
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    type: position_score
  id: hg38/TESTPosAgg
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  version: '0'
- config:
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        type: number
        view_range:
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      id: phastCons100way
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      position_aggregator: max
      type: float
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      format: tabix
      header_mode: none
      pos_begin:
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    type: position_score
  id: hg38/TESTphastCons100way
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  version: '0'
- config:
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    type: liftover_chain
  id: hg38/hg38tohg19
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