<p>Depends on the software to generate the segmentation file;</p>

<p>For example I have used scatngs for segmentation that for sample returns </p>

<pre><code>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
</code></pre>

<p>By  log2(Major copy number—tumor +  Minor copy number—tumor /ploidy of each sample) you would get segment mean</p>

<p>For number of probes </p>

<pre><code>The number of probes depends on where the data came from.
1) From SNP arrays:  Number of array probes within each segment.
2) From exon capture data:   Probes are the ends of exons and so the number of probes are equal to the number of exons  X 2.
3) 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 + 
</code></pre>

<p>For example in my case for scatngs</p>

<pre><code>Each SNP is a marker, and so you have to count how many of these SNPs are on each segment
</code></pre>

<p>I have asked this question in </p>

<p><a href="https://bioinformatics.stackexchange.com/questions/8531/extracting-the-number-snp-in-each-range?noredirect=1#comment11314_8531">Extracting the number SNP in each range</a></p>

CC BY-SA 4.0
2019-05-03T13:03:04.327Z
2019-05-03T13:03:04.327Z
Zizogolu
<p>Long time I am struggling how to provide <strong><em>GISTIC2</em></strong> required input like <code>Num_Probes</code> and <code>Segment_Mean</code></p>

<p>I have called somatic copy number by scatngs and I have copy number output file (attached); </p>

<p><a href="https://www.dropbox.com/s/r6nef2v1j2di6q6/my.copynumber.caveman.csv?dl=0" rel="nofollow noreferrer">https://www.dropbox.com/s/r6nef2v1j2di6q6/my.copynumber.caveman.csv?dl=0</a></p>

<p>This is few lines of scatngs copy number output</p>

<pre><code>1,1,13116,665401,2,1,3,1
2,1,668374,96324627,2,1,2,1
3,1,96326095,96419709,2,1,1,0
</code></pre>

<p>In scatngs reference paper says in this file we have</p>

<pre><code>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
</code></pre>

<p>scatngs also returns another output like below</p>

<p><a href="https://www.dropbox.com/s/7i28vooixdp06c2/WTSI-OESO_121_1pre.copynumber.txt?dl=0" rel="nofollow noreferrer">https://www.dropbox.com/s/7i28vooixdp06c2/WTSI-OESO_121_1pre.copynumber.txt?dl=0</a></p>

<pre><code>Chromosome  Position    Log R   segmented LogR  BAF segmented BAF   Copy number Minor allele    Raw copy number
rs62635286  1   13116   -0.0290741822638953 0.245246748556562   0.25    NA  3   1   2.35806652809599
rs75454623  1   14930   0.402869048014209   0.245246748556562   0.3095  NA  3   1   4.14031506947036
</code></pre>

<p>I am wondering how I can get <code>Num_Probes</code> and <code>Segment_Mean</code> From this files?</p>

<p>People say</p>

<pre><code>Segment_Mean = log2(tumour copy number / 2)
</code></pre>

<p>So, does that mean I should add up <code>Major copy number—tumor</code> and </p>

<p><code>Minor copy number—tumor</code> to get tumour copy number? for getting Num_Probes what should I do?</p>

<p><strong><em>EDITED</em></strong></p>

<blockquote>
  <p>people says</p>
  
  <p>scatngs uses read counts at SNPs to generate calls and so the
  locations of the SNPs is what I need to
  generate the number of markers in each segment. (eg each SNP = 1
  marker).</p>
  
  <p>Do they mean, for instance if the position of SNP  rs62635286 is
  13116, so the num_prob is 13116?</p>
</blockquote>

<p>Any help please?</p>

<p>Thanks a lot in advance </p>

CC BY-SA 4.0
2019-04-22T13:32:00.467Z
Cross-posted on GitHub for some reason: https://github.com/cancerit/ascatNgs/issues/84
Ram RS
CC BY-SA 4.0
2019-04-22T13:52:12.563Z
I mentioned a cross-post. That does not stop anyone from reading the question or helping you.
Ram RS
CC BY-SA 4.0
2019-04-22T14:16:14.390Z
Mentioning a cross post is hardly negative feedback or reason to ignore a post that belongs on bioinfo SE.
Ram RS
CC BY-SA 4.0
2019-04-23T10:32:47.040Z
Did you try reading the GISTIC2 documentation about how to get the data in that format? Or perhaps they point to a known file extension (or a weird one from only a single program) I tried searching on a couple of website about these required Num_probes but couldn't find anything. Are you using [this](ftp://ftp.broadinstitute.org/pub/GISTIC2.0/) software or other with the same name?
llrs
CC BY-SA 4.0
2019-04-23T10:36:55.660Z
I read GISTIC2 documentation, there is nothing about how to get required format. Exactly I am trying the same software you are referring to. People using GISTIC in broad institute produce their CN by this method that returns format for GISTIC https://software.broadinstitute.org/gatk/documentation/article?id=9143#1
Zizogolu
<wgs><copy-number>
Getting this information for GISTIC2
# Getting this information for GISTIC2

(Asked by: username_0 on 2019-04-22)

Long time I am struggling how to provide GISTIC2 required input like Num_Probes and Segment_Mean
I have called somatic copy number by scatngs and I have copy number output file (attached); 
https://www.dropbox.com/s/r6nef2v1j2di6q6/my.copynumber.caveman.csv?dl=0
This is few lines of scatngs copy number 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

In scatngs reference paper says in this file we have
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

scatngs also returns another output like below
https://www.dropbox.com/s/7i28vooixdp06c2/WTSI-OESO_121_1pre.copynumber.txt?dl=0
Chromosome  Position    Log R   segmented LogR  BAF segmented BAF   Copy number Minor allele    Raw copy number
rs62635286  1   13116   -0.0290741822638953 0.245246748556562   0.25    NA  3   1   2.35806652809599
rs75454623  1   14930   0.402869048014209   0.245246748556562   0.3095  NA  3   1   4.14031506947036

I am wondering how I can get Num_Probes and Segment_Mean From this files?
People say
Segment_Mean = log2(tumour copy number / 2)

So, does that mean I should add up Major copy number—tumor and 
Minor copy number—tumor to get tumour copy number? for getting Num_Probes what should I do?
EDITED

people says
scatngs uses read counts at SNPs to generate calls and so the
  locations of the SNPs is what I need to
  generate the number of markers in each segment. (eg each SNP = 1
  marker).
Do they mean, for instance if the position of SNP  rs62635286 is
  13116, so the num_prob is 13116?

Any help please?
Thanks a lot in advance

**Tags:** wgs, copy-number
> **Comments:**
> **username_1**: Cross-posted on GitHub for some reason: https://github.com/cancerit/ascatNgs/issues/84  
> **username_1**: I mentioned a cross-post. That does not stop anyone from reading the question or helping you.  
> **username_1**: Mentioning a cross post is hardly negative feedback or reason to ignore a post that belongs on bioinfo SE.  
> **username_2**: Did you try reading the GISTIC2 documentation about how to get the data in that format? Or perhaps they point to a known file extension (or a weird one from only a single program) I tried searching on a couple of website about these required Num_probes but couldn't find anything. Are you using [this](ftp://ftp.broadinstitute.org/pub/GISTIC2.0/) software or other with the same name?  
> **username_0**: I read GISTIC2 documentation, there is nothing about how to get required format. Exactly I am trying the same software you are referring to. People using GISTIC in broad institute produce their CN by this method that returns format for GISTIC https://software.broadinstitute.org/gatk/documentation/article?id=9143#1  

---

## 1 answers

### Answer by username_0 on 2019-05-03. Score: 0 | Accepted answer

Depends on the software to generate the segmentation file;
For example I have used scatngs for segmentation that for sample returns 
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

By  log2(Major copy number—tumor +  Minor copy number—tumor /ploidy of each sample) you would get segment mean
For number of probes 
The number of probes depends on where the data came from.
1) From SNP arrays:  Number of array probes within each segment.
2) From exon capture data:   Probes are the ends of exons and so the number of probes are equal to the number of exons  X 2.
3) 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 + 

For example in my case for scatngs
Each SNP is a marker, and so you have to count how many of these SNPs are on each segment

I have asked this question in 
Extracting the number SNP in each range


---

