---

type: allele_score

table: 
  filename: gnomad.exomes.r2.1.1.extract.tsv.gz
  format: tabix

  # defined by score_type
  # VCF like variant description
  chrom:
    name: CHROM
  pos_begin:
    name: POS
  pos_end:
    name: POS
  reference:
    name: REF
  alternative:
    name: ALT

# score values
scores:
  - id: ID
    name: ID
    type: str
    desc: "gnomAD v2.1.1 liftover exomes variant ID"
  - id: AC
    name: AC
    type: int
    desc: "Alternative allele count in the whole gnomAD exome samples v2.1.1"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0
        max: 260000
      y_log_scale: True
  - id: AN
    name: AN
    type: int
    desc: "Total allele count in the whole gnomAD exome samples v2.1.1"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0
        max: 260000
      y_log_scale: True
  - id: AF
    name: AF
    type: float
    desc: "Alternative allele frequency in the whole gnomAD exome samples v2.1.1"
    histogram:
      type: number
      number_of_bins: 126
      view_range:
        min: 0.0
        max: 1.0
      y_log_scale: True
      x_log_scale: True
      x_min_log: 0.00001

  - id: AF_percent
    name: AF_percent
    type: float
    desc: "Alternative allele frequency in the whole gnomAD exome samples v2.1.1 as %"
    histogram:
      type: number
      number_of_bins: 126
      view_range:
        min: 0.0
        max: 100.0
      y_log_scale: True
      x_log_scale: True
      x_min_log: 0.001

  - id: controls_AC
    name: controls_AC
    type: int
    desc: "Alternative allele count in the controls subset of whole gnomAD exome samples v2.1.1"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0
        max: 120000
      y_log_scale: True

  - id: controls_AN
    name: controls_AN
    type: int
    desc: "gnomAD v2.1.1 liftover exomes count of genotyped individuals in control group"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0
        max: 120000
      y_log_scale: True
  - id: controls_AF
    name: controls_AF
    type: float
    desc: "Alternative allele frequency in the controls subset of whole gnomAD exome samples v2.1.1"
    histogram:
      type: number
      number_of_bins: 126
      view_range:
        min: 0.0
        max: 1.0
      y_log_scale: True
      x_log_scale: True
      x_min_log: 0.00001
  - id: controls_AF_percent
    name: controls_AF_percent
    type: float
    desc: "Alternative allele frequency in the controls subset of whole gnomAD exome samples v2.1.1 as %"
    histogram:
      type: number
      number_of_bins: 126
      view_range:
        min: 0.0
        max: 100.0
      y_log_scale: True
      x_log_scale: True
      x_min_log: 0.001
  - id: non_neuro_AC
    name: non_neuro_AC
    type: int
    desc: "Alternative allele count in the non-neuro subset of whole gnomAD exome samples v2.1.1"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0
        max: 210000
      y_log_scale: True

  - id: non_neuro_AN
    name: non_neuro_AN
    type: int
    desc: "Total allele count in the non-neuro subset of whole gnomAD exome samples v2.1.1"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0
        max: 210000
      y_log_scale: True

  - id: non_neuro_AF
    name: non_neuro_AF
    type: float
    desc: "Alternative allele frequency in the non-neuro subset of whole gnomAD exome samples v2.1.1"
    histogram:
      type: number
      number_of_bins: 126
      view_range:
        min: 0.0
        max: 1.0
      y_log_scale: True
      x_log_scale: True
      x_min_log: 0.00001

  - id: non_neuro_AF_percent
    name: non_neuro_AF_percent
    type: float
    desc: "Alternative allele frequency in the non-neuro subset of whole gnomAD exome samples v2.1.1 as %"
    histogram:
      type: number
      number_of_bins: 126
      view_range:
        min: 0.0
        max: 100.0
      y_log_scale: True
      x_log_scale: True
      x_min_log: 0.001


# default annotation
default_annotation:
  - source: AF_percent
    name: exome_gnomad_v2_1_1_af_percent
  - source: AC
    name: exome_gnomad_v2_1_1_ac
  - source: AF
    name: exome_gnomad_v2_1_1_af
  - source: AN
    name: exome_gnomad_v2_1_1_an
  - source: controls_AC
    name: exome_gnomad_v2_1_1_controls_ac
  - source: controls_AN
    name: exome_gnomad_v2_1_1_controls_an
  - source: non_neuro_AC
    name: exome_gnomad_v2_1_1_non_neuro_ac
  - source: non_neuro_AN
    name: exome_gnomad_v2_1_1_non_neuro_an
  - source: controls_AF_percent
    name: exome_gnomad_v2_1_1_controls_af_percent
  - source: non_neuro_AF_percent
    name: exome_gnomad_v2_1_1_non_neuro_af_percent


meta: 
  summary: |

    Liftover of gnomAD exomes v2.1.1 to hg38.

  description: |
    ## gnomAD exomes v2.1.1 liftover

    Liftover of gnomAD exomes v2.1.1 to hg38 published by the Broad Institute.

    Original gnomAD exomes v2.1.1 liftover is downloaded on October 19, 2020.

  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
