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  • Paralleling Control-FREEC chromosome by chromosome

    I'm wondering if anyone is an expert on Control-FREEC here.

    I've used this config file to run Control-FREEC on a tumor-normal WGS data:

    Code:
    [general]
    
    BedGraphOutput = TRUE
    breakPointThreshold = 0.8
    breakPointType=2
    chrLenFile = /PATH/TO/b37.len
    chrFiles = /PATH/TO/b37/contigs
    coefficientOfVariation = 0.05
    contaminationAdjustment = TRUE
    gemMappabilityFile = /PATH/TO/out100m2_hg19.gem
    minMappabilityPerWindow = 0.85
    forceGCcontentNormalization = 2
    ploidy = 2
    intercept = 0
    minCNAlength = 4
    outputDir = /PATH/TO/control_freec_experiment/setting_03c
    degree=3
    maxThreads = 2
    #readCountThreshold=10
    samtools = samtools
    sex = XX
    #telocentromeric=50000
    uniqueMatch=TRUE
    
    
    [sample]
    
    mateFile = /PATH/TO/wgs.tumor.pileup
    inputFormat = pileup
    mateOrientation = FR
    
    
    [control]
    
    mateFile = /PATH/TO/wgs.normal.pileup
    inputFormat = pileup
    mateOrientation = FR
    
    
    [BAF]
    
    SNPfile = /PATH/TO/hg19_snp131.SingleDiNucl.1based.txt
    minimalCoveragePerPosition = 5

    It worked well, but what I would really love to do, is to parallelize the process more, and process more of the data chromosome-by-chromosome if possible.

    Is there a good way to do that?
    For instance, is there a good way to generate the .cpn file chromosome by chromosome first, and then combine the .cpn files, then call CNV using those combined .cpn files?

    Thanks in advance for any help and suggestion!

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