This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Using Control-FREEC for detecting CNV and LOH for paired normal/tumor samples

I would like to have some suggestions from the users of control-FREEC, I have the normal and tumor bam files, now to run the freec on them I need to create the config file first right? Below is the config file that can be used to run with control sample

[general]

chrLenFile = hs18_chr.len
coefficientOfVariation = 0.062
ploidy = 3

#breakPointThreshold = -.002;
#window = 50000
#chrFiles = hg18/hg18_per_chromosome
#outputDir = test
#degree=3
#intercept = 0

[sample]

mateFile = HCC1143.arachne
inputFormat = arachne
mateOrientation = 0

#mateCopyNumberFile = HCC1143.arachne_sample.cpn

[control]

mateFile = HCC1143_BL.arachne
inputFormat = arachne
mateOrientation = 0

#mateCopyNumberFile = HCC1143_BL.arachne_control.cpn

How shall the modify them with my tumor and normal samples. Will this work if I simply put the corresponding bam files or do I have to put the pileup files here in the control and the tumor samples. Also I would like to know if anyone would like to share a working script which I can refer to modify and use it with my samples. If you are not aware of the ploidy then how will it affect the output. I do not have the ploidy status for my samples, probably am assuming that it is different from the diploid status, but in this config file do I have to know the exact ploidy of the tumor sample? I would like to have some suggestions, please ask me things which are not clear.

cnv snp r control-freec next-gen
• 1,002 views • link
updated by Ram Ram • written by ivivek_ngs ivivek_ngs

I am unable to extract the GEM_mapp_hg19.tar.gz with tar xvzf command. Can anyone tell me for the Control-FREEC can we supply the .gz file directly or do we need to extract it?

• 0 views • link
updated by Ram Ram • written by ivivek_ngs ivivek_ngs

It seems that the file was corrupted while transferring now it works. One more question, for my data the paired end exome sequencing was done with 100 bp , so I should be using this hg19_len100bp.tar.gz right? But this file is strikingly smaller in size, can anyone tell me why?

• 0 views • link
updated by Ram Ram • written by ivivek_ngs ivivek_ngs

It seems there were 3 .gem files in GEM_mapp_hg19.tar.gz. However in the hg19_len100bp.tar.gz I see two files, which should I use?

out100m2_hg19.gem and out100m1_hg19.gem

• 0 views • link
updated by Ram Ram • written by ivivek_ngs ivivek_ngs

0 answers

No answers yet.

Log in to answer this question.

More posts like this