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

[general]
bedtools = /home/x_seoju/bedtools2/bin/bedtools
breakPointThreshold = 0.6
breakPointType = 2
chrFiles = /proj/sc_ml/regev/reference/GRCh37/Ensembl/chromosomes/
chrLenFile = /proj/sc_ml/regev/reference/GRCh37/Ensembl/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.fai
maxThreads=8
outputDir = /proj/sc_ml/regev/bulk-wes/CY79/
ploidy = 2
printNA=FALSE
#readCountThreshold = 50
sambamba = /home/x_seoju/sambamba/bin/sambamba-0.7.1
samtools = /home/x_seoju/bin/samtools-1.3/samtools
sex = XY
step = 50
window = 100

[sample]

mateFile = /proj/sc_ml/regev/bulk-wes/CY79/79_Tumor.bam
inputFormat = bam
mateOrientation = FR

[control]

mateFile = /proj/sc_ml/regev/bulk-wes/CY79/79_Normal.bam
inputFormat = bam
mateOrientation = FR