Open zhangb1 opened 5 years ago
Probably there was an update on the way how the baseline is calculated (corresponding to copy neutral state) and this causes the differences.. If your input is "pileup" there will be changed due file processing..
So maybe you can share with me the corresponding config and the output into the command line so that I could see where the difference comes from?
Also, did you try to visualize the output as .png and see how it compares?
[general]
chrLenFile = /home/ubuntu/volume/control-freeC/hs38_chr.len
ploidy = 2,3,4
chrFiles = ./GRCh38_everyChrs
maxThreads = 32
outputDir = ./
sambamba = /home/ubuntu/bin/sambamba
samtools = /home/ubuntu/bin/samtools
coefficientOfVariation = 0.062
[sample]
mateFile = /home/ubuntu/volume/control-freeC/e2ef44aa-10a8-474e-a897-f5e1b47ac587.bam
inputFormat = BAM
mateOrientation = FR
[control]
mateFile = /home/ubuntu/volume/control-freeC/6b7ea15f-050f-41ab-b0b3-24073331c77f.bam
inputFormat = BAM
mateOrientation = FR
Thanks @valeu , I put the configure file here, correction, I set both the ploidy to 2,3,4
not 2
.
and the png file is here:
version 8.7
version 11.5
Thanks again
What ploidy was selected by FREEC as the best one? Version 11.5 will write it into an info.txt file. For version 8.7 you may have to look into the command line.
Version 11.5 have the info.txt file. Output_Ploidy is 2, but v8.7 I can't find the information in the command line and output.
Program_Version v11.5
Sample_Name e2ef44aa-10a8-474e-a897-f5e1b47ac587.bam
Control_Used True
CGcontent_Used False
Mappability_Used False
Looking_For_Subclones False
Breakpoint_Threshold 0.8
Window 401
Number_Of_Reads|Pairs_In_Sample 1939499214
Number_Of_Reads|Pairs_In_Control 911816637
Output_Ploidy 2
Sample_Purity 1
Good_Polynomial_Fit True
Then just post the complete output here, and I will tell you..
Thanks , I attached CNVs result here, this is from version 8.7 e2ef44aa-10a8-474e-a897-f5e1b47ac587.bam_CNVs.zip
It is weird. It looks like v8.7 selected 2 as the main ploidy.. Must be something in the code that has been corrected since..
Hi ,
I used both v8.7 and v11.5 to run the same WGS sample. and set the ploidy to 2.
but we got the completed different results for the ratio.txt
v8.7
v11.5
Do you know why ?and did you update the method for ratio calculation?
Thanks