CNV_Radar_config.yml

# Number of iterations for reweighting
iter: 3
# Number of knots, max of 20 or the length of the chromosome/params$smooth per chromosome
smooth: 4
# If the difference of the log2FC between two adjacent points are less than params$collapse then merge into one call
collapse: 0.1
# Minimum depth required to call a variant
minVarDepth: 25
# Minimum predicted depth required to call a CNV event
minExpDepth: 10
# To resolve the focality of the cutpoint using a window of size +/- params$m around the cutpoint
focal_thresh: 100
# Sensitivity threshold, Upper threshold for the Q score of a CNV event
threshHigh: 0.04
# Sensitivity threshold, the predictive score is less than params$threshLow, for detecting cnvs on the last iteration
threshLow: -0.1
# For a called CNV event, to call an LOH event the log2 fold change must be greater than params$theshFC_Low
threshFC_Low: -0.25
# For a called CNV event, to call an LOH event the log2 fold change must be greater than params$theshFC_High
threshFC_High: 0.2
# Lower heterozygous allele frequency threshold for calling an LOH event in a 'neutral' region
LOHthresh: 0.05
# Minimum CNV event length threshold in bases for calling an LOH event in a 'neutral' region
LOHminLength: 2000

overlap:
    # Remove redundant breakpoints, if there is params$overlap in raw fold change estimates between adjacent regions
    HIGH_SENSITIVITY: 0.2
    STANDARD_SENSITIVITY: 0.1