---

type: allele_score
allele_score_mode: substitutions

table:
  filename: CADD.bedgraph.gz
  format: tabix

  header_mode: none

  # defined by score_type
  chrom:
    index: 0
  pos_begin:
    index: 1
  pos_end:
    index: 1
  reference:
    index: 2
  alternative:
    index: 3

# score values
scores:
  - id: cadd_raw
    index: 4
    type: float
    desc: |
      CADD raw score for functional prediction of a SNP. The larger the score 
      the more likely the SNP has damaging effect
    large_values_desc: "more damaging"
    small_values_desc: "less damaging"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: -8.0
        max: 36
      y_log_scale: True

  - id: cadd_phred
    index: 5
    type: float
    desc: |
      CADD phred-like score. This is phred-like rank score based on whole
      genome CADD raw scores. The larger the score the more likely the SNP
      has damaging effect.
    large_values_desc: "more damaging"
    small_values_desc: "less damaging"
    histogram:
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0.0
        max: 99.0
      y_log_scale: True

default_annotation:
  - source: cadd_raw
    name: cadd_raw
  - source: cadd_phred
    name: cadd_phred

meta:
  summary: |
    CADD score for functional prediction of a SNP

  description: |
    ## CADD
    Please refer to Kircher
    et al. (2014) Nature Genetics 46(3):310-5 for details. The larger the score the
    more likely the SNP has damaging effect. 

    Downloaded from https://cadd.gs.washington.edu/download ;
    
    Higher values of raw scores
    have relative meaning that a variant is more likely to be simulated (or 
    "not observed") and therefore more likely to have deleterious effects.
    
    Scaled scores are PHRED-like (-10*log10(rank/total)) scaled C-score ranking
    a variant relative to all possible substitutions of the
    human genome (8.6x10^9).

    Please note the following copyright statement for CADD: "CADD scores
    (http://cadd.gs.washington.edu/) are Copyright 2013 University of Washington and
    Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely
    available for all academic, non-commercial applications. For commercial licensing
    information contact Jennifer McCullar (mccullaj@uw.edu).

  labels:
    reference_genome: hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174
