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###For more options see: http://boevalab.com/FREEC/tutorial.html#CONFIG ###
[general]
##parameters chrLenFile and ploidy are required.
chrLenFile = test/hg19.fa.fai
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/hg19/
#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
#readCountThreshold=10
#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 = 0
#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
##use "mateOrientation=0" for sorted .SAM and .BAM
[control]
#mateFile = /path/control.pileup.gz
#mateCopyNumberFile = path/control.cpn
#inputFormat = pileup
#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
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