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###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