Purity and ploidy in CNV analysis

[beginner984]

Thank you for this tool

In copy number analysis from scatngs for each sample I have these outputs

**copynumber.caveman.csv

copynumber.txt

samplestatistics.txt**

Can I use purity and ploidy mentioned in output picture for example from information in this plot, I really need this information

Thank you for any help

[keiranmraine]

Please see the wiki for details of the protocols paper which covers interpretation of results.

[beginner984]

Sorry,

This is a few lines of my copynumber.caveman.csv output

1   1   13116   665401          2   1   3   1
2   1   668374  96324627    2   1   2   1
3   1   96326095 96419709   2   1   1   0
4   1   96421112 103508275  2   1   2   1

In protocol paper says

copynumber.caveman.csv  Comma-separated values  Simple form of copy number segments in format:

    Segment number

    Chromosome

    Start position (origin-1)

    End position (origin-1)

    Major copy number—normal

    Minor copy number—normal

    Major copy number—tumor

    Minor copy number—tumor

How I can get such information from my file

Chromosome  Start   End Total_CN    Minor_CN
1   10583   1017587 3   1
1   1018144 2466425 5   2
1   2475113 7770901 3   1

People say

If I want to use scatngs output to calculate the seg mean by doing this. 1) Add up the total copy number to get tumor copy number. 2) Segment_Mean = log2(tumor copy number / tumor ploidy). I could use 2 instead of tumor ploidy if I am sure that all of mytumors are diploid and have not gone through genomic doubling.

The number of probes depends on where the data came from.

From whole genome sequencing: Probes are the boundaries of bins used to generate the copy number data and so the number of probes are equal to the number of bins + 1.

But I don't know how to get the boundaries of bins used to generate the copy number data

Any help please?

WTSI-OESO_121_1pre.copynumber.caveman.txt

[RamRS]

But my first column does not seem to be total copy number

Because it is not. The protocol paper clearly says (from what you pasted) that the first column is Segment number.