wisecondorx.yaml

# Use --header with this config
chrom:
  value: $chr
  prefix: chr
pos:
  value: $start
id:
  prefix: wisecondorx_
alt:
  value: ~if $type == loss <DEL> <DUP>
  options:
    - name: DEL
      description: "Deletion"
    - name: DUP
      description: "Duplication"
    - name: CNV
      description: "Copy number variation"
info:
  - name: CNV_RATIO
    value: $ratio
    type: float
    number: 1
    description: "Copy number ratio"
  - name: ZSCORE
    value: $zscore
    type: float
    number: 1
    description: "The z-score of the variant"
  - name: SVTYPE
    value: CNV
    type: string
    number: 1
    description: "The type of structural variant"
  - name: END
    value: $end
    type: integer
    number: 1
    description: "End position of the variant"
  - name: SVLEN
    value: ~min $end $start -1
    type: integer
    number: 1
    description: "The total length of the structural variant"
  - name: CALLERS
    value: wisecondorx
    type: string
    number: .
    description: "The callers used to determine this variant"
format:
  - name: GT
    value: "."
    type: string
    number: 1
    description: "Genotype"
  - name: CN
    value: ~round $ratio
    type: integer
    number: 1
    description: "Copy number"