config_file_FREEC

[general]

chrLenFile = /scratch/GT/vdas/pietro/exome_seq/test_Control_FREEC/hs19_chr.len
window = 500

step = 250
ploidy = 2
readCountThreshold = 50
sex=XX
outputDir = /scratch/GT/vdas/pietro/exome_seq/results/control_freec_out/output5_S313_tumor/
BedGraphOutput=TRUE
breakPointType=4

gemMappabilityFile = /scratch/GT/vdas/pietro/exome_seq/test_Control_FREEC/out100m1_hg19.gem

chrFiles =  /scratch/GT/vdas/test_exome/exome/

maxThreads=6
minCNAlength=2
minMappabilityPerWindow=0.85
breakPointThreshold = 1.5
noisyData=TRUE
printNA=FALSE
intercept = 0 
[sample]

mateFile = /scratch/GT/vdas/pietro/exome_seq/results/T_S7998/T_S7998.realigned.recal.pileup
inputFormat = pileup
mateOrientation = FR

[control]

mateFile = /scratch/GT/vdas/pietro/exome_seq/results/N_S8980/N_S8980.realigned.recal.pileup
inputFormat = pileup
mateOrientation = FR

[BAF]

SNPfile = /scratch/GT/vdas/pietro/exome_seq/test_Control_FREEC/hg19_snp142.SingleDiNucl.1based.txt
minimalCoveragePerPosition = 5
minimalQualityPerPosition = 20
shiftInQuality = 33

[target]

captureRegions = /scratch/GT/vdas/referenceBed/hg19/ss_v4/Exon_SSV4_clean.bed