Hello everybody !
I am using Control freec (FREEC v6.4 (Control-FREEC v3.4) ) on exome paired (tumor-control) data, on about 25 patients.
I have several issues I would like to share here to get some help hopefully.
First, for CNV of the control sample, I got a line at 2 for all my 25 patients (attached file "CNV.mpileup_normal_ratio.txt.png"). I wonder why there is no noise around 2 and why I cannot get points as I do for the tumor sample (attached file "CNV.mpileup_ratio.txt.png"). I changed the option noisyData but it doesn't seem to be the explanation.
My second problem is for the BAF calculations. As you can see in the control ("baf.mpileup_normal_BAF.txt.png") sample (it's the same for tumor), there is something wrong on chromosome 7, for all patients. There is one point after the end of chromosome. I don't understand why. I can see indeed this point in the BAF.txt file :
Finally, for some patients, I have anarchical results (see example2). All my patients have the same pathology (a leukemia), so I doubt that such karyotypes are true... I am wondering if these kind of results are not the consequence of altered DNA...
Could you please tell me if you faced one of these problems and how did you solve it?
Thank you in advance,
Jane
I am using Control freec (FREEC v6.4 (Control-FREEC v3.4) ) on exome paired (tumor-control) data, on about 25 patients.
I have several issues I would like to share here to get some help hopefully.
First, for CNV of the control sample, I got a line at 2 for all my 25 patients (attached file "CNV.mpileup_normal_ratio.txt.png"). I wonder why there is no noise around 2 and why I cannot get points as I do for the tumor sample (attached file "CNV.mpileup_ratio.txt.png"). I changed the option noisyData but it doesn't seem to be the explanation.
My second problem is for the BAF calculations. As you can see in the control ("baf.mpileup_normal_BAF.txt.png") sample (it's the same for tumor), there is something wrong on chromosome 7, for all patients. There is one point after the end of chromosome. I don't understand why. I can see indeed this point in the BAF.txt file :
7 94855040 0.6 0.5 0.5 0.5 0.5 19.905
7 94937446 0.47619 0.5 0.5 0.5 0.5 19.905
7 94941038 0.5 -1 2 -1 2 -1
7 892613944 1.07685e-08 0.5 0.5 0.324618 0.675382 0.5
8 182807 0.333333 -1 2 -1 2 -1
7 94937446 0.47619 0.5 0.5 0.5 0.5 19.905
7 94941038 0.5 -1 2 -1 2 -1
7 892613944 1.07685e-08 0.5 0.5 0.324618 0.675382 0.5
8 182807 0.333333 -1 2 -1 2 -1
Could you please tell me if you faced one of these problems and how did you solve it?
Thank you in advance,
Jane
Comment