combine-callers.yaml

# Tweak ensemble parameters when combinining inputs from multiple calling methods.
# These feeds into the `variant-ensemble` task which provides a simplified
# interface for generating ensemble calls.
---
ensemble:
  # Baseline filters to apply to combined calls.
  format-filters: [DP < 4, QUAL < 5]
  # Variants present in this percentage of input samples automatically pass
  trusted-pct: 0.65
  # Variables to use in classifying reads not in the trusted group.
  # You can specify any number of classifier groups, each of which will be evaluated separately.
  classifiers:
    general: [AD, PL, DP]
  classifier-params:
    type: svm
# Optional names to label the input variant calls
# If not supplied, default to numbers matched with the VCF inputs (v0, v1)
names: ['gatk', 'freebayes']
# Perform prep and pre-cleaning steps. Set to false if inputs are pre-sorted
# and filtered to save analysis time.
prep-inputs: true
# Optional path to BED file of regions to analyze
# intervals: /path/to/intervals.bed