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:
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!
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!