###For more options see: http://boevalab.com/FREEC/tutorial.html#CONFIG ###

[general]
chrLenFile = hg19.fa.fai
window = 0
ploidy = 2,3
outputDir = /myOutputDirectory/

#sex=XY
breakPointType=4
chrFiles =  /pathToChromosomeFastaFiles/Human/hg19/chromosomes/

maxThreads=6

breakPointThreshold=1.2
noisyData=TRUE
printNA=FALSE

readCountThreshold=50

[sample]

mateFile = /data/Tumor.onTarget.q20.nodup.pileup.gz
inputFormat = pileup
mateOrientation = 0

[control]

mateFile = /data/Normal.onTarget.q20.nodup.pileup.gz
inputFormat = pileup
mateOrientation = 0

[BAF]

SNPfile = /bioinfo/users/vboeva/Desktop/annotations/hg19_snp131.SingleDiNucl.1based.txt
minimalCoveragePerPosition = 5

[target]

captureRegions = /EXOME-SEQ/TruSeq_exome_targeted_regions.hg19.bed

