Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-03T13:03:04.327Z
Answers.LastActivityDate: 2019-05-03T13:03:04.327Z
Answers.UserDisplayName: Zizogolu
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-22T13:32:00.467Z
Comments.Text: Cross-posted on GitHub for some reason: https://github.com/cancerit/ascatNgs/issues/84
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-22T13:52:12.563Z
Comments.Text: I mentioned a cross-post. That does not stop anyone from reading the question or helping you.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-22T14:16:14.390Z
Comments.Text: Mentioning a cross post is hardly negative feedback or reason to ignore a post that belongs on bioinfo SE.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-23T10:32:47.040Z
Comments.Text: 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?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-23T10:36:55.660Z
Comments.Text: 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
Comments.UserDisplayName: Zizogolu
Tags: <wgs><copy-number>
Title: Getting this information for GISTIC2
ThreadText: # 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](https://bioinformatics.stackexchange.com/questions/8531/extracting-the-number-snp-in-each-range?noredirect=1#comment11314_8531)
  
  
  ---
  
  