[general]


#parameters chrLenFile and ploidy are required.

chrLenFile = test/hs18_chr.len
ploidy = 2


#Parameter "breakPointThreshold" specifies the maximal slope of the slope of residual sum of squares. 
#This should be a positive value. The closer it is to Zero, the more breakpoints will be called. Its recommended value is between 0.01 and 0.08.

breakPointThreshold = .8


#Either coefficientOfVariation or window must be specified for whole genome sequencing data. Set window=0 for exome sequencing data.

#coefficientOfVariation = 0.01
window = 50000
#step=10000


#Either chrFiles or GCcontentProfile must be specified too if no control dataset is available. 
#If you provide a path to chromosome files, Control-FREEC will look for the following fasta files in your directory (in this order): 
#1, 1.fa, 1.fasta, chr1.fa, chr1.fasta; 2, 2.fa, etc.
# Please ensure that you don't have other files but sequences having the listed names in this directory. 
chrFiles = path/hg18
#GCcontentProfile = test/GC_profile_50kb.cnp


#if you are working with something non-human, we may need to modify these parameters:
#minExpectedGC = 0.35
#maxExpectedGC = 0.55


#numberOfProcesses = 4
#outputDir = test
#contaminationAdjustment = TRUE
#contamination = 0.4
#minMappabilityPerWindow = 0.95


#If the parameter gemMappabilityFile is not specified, then the fraction of non-N nucleotides per window is used as Mappability.

#gemMappabilityFile = /GEM_mappability/out76.gem


#breakPointType = 4
#forceGCcontentNormalization = 1
#sex=XY

#set BedGraphOutput=TRUE if you want to create a BedGraph track for visualization in the UCSC genome browser:
#BedGraphOutput=TRUE

[sample]

mateFile = /path/sample.bam

#mateCopyNumberFile = test/sample.cpn
inputFormat = BAM
mateOrientation = RF

[control]

#mateFile = /path/control.sam
#mateCopyNumberFile = path/control.cpn
#inputFormat = SAM

#use "mateOrientation=0" for sorted .SAM and .BAM

#mateOrientation = RF


#[BAF]

#use the following options to calculate B allele frequency profiles and genotype status. This option can only be used if "inputFormat=pileup"

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

#use "minimalQualityPerPosition" and "shiftInQuality" to consider only high quality position in calculation of allelic frequencies (this option significantly slows down reading of .pileup)

#minimalQualityPerPosition = 5
#shiftInQuality = 33

[target]

#use a tab-delimited .BED file to specify capture regions (control dataset is needed to use this option):

#captureRegions = /bioinfo/users/vboeva/Desktop/testChr19/capture.bed