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Old 05-18-2012, 12:52 PM   #19
bw.
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Location: San Francisco, CA

Join Date: Mar 2012
Posts: 21
Default Calling CNA and BAF for exome seq data without a control

Hi, I'm trying to use FREEC to call CNA and BAF in some exome seq samples, but haven't been able to make it work. The tool ran fine on the chr19 test data.

The problems I'm seeing are
- the tool runs but doesn't generate any of the output files except mpileup.txt_sample.cpn
It exits with the error message:
..There is no control sample!!!
You have to use a matching control sample to get adequite results since GC-bias is not the only bias in targeted sequencing

- even the .cpn file doesn't seem right because it tries to call copy number outside the target regions I provided via the TruSeq_exome_targeted_regions.hg19.bed
and not surprisingly calls them all as 0 copy number.


I'm running the tool on a pileup generated using samtools v.0.1.12. I'm using the following config file:


[general]
chrLenFile=hg19.len

window = 3000
step = 1000
ploidy = 2

#breakPointThreshold = -.001

#GCcontentProfile = GC_profile.cnp

intercept=1
minMappabilityPerWindow = 0.7

outputDir = .

sex=XY
breakPointType=4

#degree=3
#coefficientOfVariation = 0.05
#gemMappabilityFile = /hg19/out76_hg19.gem

chrFiles = FREEC_Linux64/chromosomes/

[sample]

mateFile=mpileup.txt
#mateCopyNumberFile=mpileup.txt_sample.cpn

inputFormat = pileup
mateOrientation = FR

[control]

[BAF]

SNPfile = hg19_snp131.SingleDiNucl.1based.txt
minimalCoveragePerPosition = 5


[target]
captureRegions=TruSeq_exome_targeted_regions.hg19.bed
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