controlfreec_config_file_example_hg19.txt

[general]

ploidy = 2,4     

window=40000
step=20000

breakPointThreshold=0.65   
breakPointType=2 

samtools=/path/to/samtools

chrLenFile=/path/to/hg19.len 
gemMappabilityFile=/path/to/hg19.gem_file 
uniqueMatch=FALSE   	

contaminationAdjustment=TRUE               

chrFiles=/path/to/hg19_chromFa
     
forceGCcontentNormalisation=1

outputDir=/path/to/outputDir

BedGraphOutput=FALSE

[sample]

mateFile=/path/to/example.bam
inputFormat=BAM  
matesOrientation=FR