ratio in *ratio.txt changed in new version 11.5?

[zhangb1]

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

1   9224    -1  -1  4
1   9625    1.1089  1.81838 4
1   10026   1.47699 1.81838 4
1   10427   0.712093    1.81838 4
1   10828   1.84898 1.81838 4
1   11229   2.08814 1.81838 4
1   11630   2.55697 1.81838 4

v11.5

1   9224    -1  -1  2
1   9625    0.68999 1.11312 2
1   10026   0.919025    1.11312 2
1   10427   0.443084    1.11312 2
1   10828   1.15048 1.11312 2
1   11229   1.2993  1.11312 2
1   11630   1.59102 1.11312 2

Do you know why ?and did you update the method for ratio calculation?

Thanks

[valeu]

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?

[zhangb1]

[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

[valeu]

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.

[zhangb1]

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

[valeu]

Then just post the complete output here, and I will tell you..

[zhangb1]

Thanks , I attached CNVs result here, this is from version 8.7 e2ef44aa-10a8-474e-a897-f5e1b47ac587.bam_CNVs.zip

[valeu]

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..