Re: SEG file for Canopy?

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Jiang, Yuchao

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Dec 6, 2018, 8:06:38 PM12/6/18
to Bao, Chunyang, canopy_phylogeny, Jiang, Yuchao
Hi Chunyang,

Thanks for your interest in Canopy and truly sorry for my late reply. We’ve encountered a potential issue in transforming the B allele frequency and the log-r ratio values from Sequenza to WM and Wm matrices, due to the ploidy issue. However, as stated in our manual, “The B-allele frequency is Bf = Wm / (WM + Wm) and the depth ratio is depth.ratio = (WM + Wm)/2. From here the input matrix WM and Wm can be calculated. “. Maybe you can try Falcon or Falcon-X? This is by default the caller in our pipeline MARATHON https://github.com/yuchaojiang/MARATHON.

Hope this can be helpful to you.
Yuchao


On Nov 9, 2018, at 3:26 PM, Bao, Chunyang <Chunya...@DFCI.HARVARD.EDU> wrote:

Hi Yuchao,
 
Thanks for your excellent work on Canopy!  I am sort of interested in it and wondering if you could give me some advice.
 
Say that I have an Allelic CNV SEG file from GATK4/ABSOLUTE, like the output of Sequenza.  After reviewing the following documents, I am still not 100% sure how to generate WM and Wm matrices from my allelic SEG file.  Do you have any tools to do that automatically for Sequenza? Or, are you still working on it? Any suggestions are welcome.
 
Documents I have read (Did I missed something …?):
 
My SEG file:
Chromosome
Start.bp
End.bp
n_probes
length
seg_sigma
W
total_copy_ratio
modal_total_cn
expected_total_cn
total_HZ
total_amp
corrected_total_cn
rescaled_total_cn
bi.allelic
copy.ratio
allele1
allele2
1
10001
16900000
2570
16889999
0.01006
0.00604
1.00758
2
2
0
0
2
2.024116
0
1.00758
0.95453
1.06064
1
16900001
17275000
52
374999
0.04017
0.00013
1.03415
2
2
0
0
2
2.114113
0
1.03415
0.74009
1.32821
1
17275001
1.21E+08
18594
1.04E+08
0.01213
0.037251
1.00447
2
2
0
0
2
2.013581
0
1.00447
0.99794
1.01101
 
 
Thanks,
Chunyang
 
 
-- 
Chunyang Bao, Ph.D.
Research Fellow
Dana-Farber Cancer Institute
Harvard Medical School
Broad Institute

Dana 857A 
450 Brookline Avenue
Boston, MA 02215-5450
617-632-2477 (office)
617-582-9830 (fax) 
 
 

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