Body: <p>I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is <em><strong>category</strong></em>.</p>
  <p>According to <a href="http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/MutSigCV" rel="nofollow noreferrer">MutSigCV</a>, every mutation can be divided into the following categories:</p>
  <ol>
  <li>CpG transitions</li>
  <li>CpG transversions</li>
  <li>C: G transitions</li>
  <li>C: G transversions</li>
  <li>A: T transitions</li>
  <li>A: T transversions</li>
  <li>null+indel mutations</li>
  </ol>
  <p>I am very much clear about some of this categories like C: G transitions and A: T transitions but for rest, I am unable to make any solid conceptual background. Can anyone suggest me the proper definition of these categories of mutations with proper examples?</p>
  <p>Thanks.</p>
  <hr />
  <p>Definition</p>
  <p>MutSig stands for &quot;Mutation Significance&quot; and is defined <a href="https://software.broadinstitute.org/cancer/cga/mutsig" rel="nofollow noreferrer">here</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-09T11:39:13.620Z
Comments.Text: Did you try asking on the [help forum](https://groups.google.com/forum/#!forum/genepattern-help)? Or your problem is what is each mutation?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-09T12:35:23.157Z
Comments.Text: @Llopis: Not yet. I even didn't know about that. I know only GATK forum and this website. I have googled these terms extensively but didn't get even proper definitions. That's why I started the bounty on this question.
Comments.UserDisplayName: Lot_to_learn
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-10T14:43:55.960Z
Comments.Text: CpG transversions are the same as C: G transversions, except that they are followed by a G which means they are potential targets for DNA methylation. Methylcytosine can undergo deamination to Thymine, which makes them mutation hotspots
Comments.UserDisplayName: heathobrien
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-10T14:49:35.197Z
Comments.Text: indel = insertion/deletion. I have no idea what null means in this context
Comments.UserDisplayName: heathobrien
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-11T09:03:31.970Z
Comments.Text: @heathobrien Those comments are an answer! With a link to a source you could get the bounty
Comments.UserDisplayName: llrs
Tags: <genomics><cancer><gatk><mutations>
Title: Meaning of category in MutSigCV
ThreadText: # Meaning of category in MutSigCV
  
  (Asked by: username_0 on 2018-07-05)
  
  I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is ***category***.
  
  According to [MutSigCV](http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/MutSigCV), every mutation can be divided into the following categories:
  
  1. CpG transitions
  2. CpG transversions
  3. C: G transitions
  4. C: G transversions
  5. A: T transitions
  6. A: T transversions
  7. null+indel mutations
  
  I am very much clear about some of this categories like C: G transitions and A: T transitions but for rest, I am unable to make any solid conceptual background. Can anyone suggest me the proper definition of these categories of mutations with proper examples?
  
  Thanks.
  
  ---
  
  Definition
  
  MutSig stands for "Mutation Significance" and is defined [here](https://software.broadinstitute.org/cancer/cga/mutsig)
  
  **Tags:** genomics, cancer, gatk, mutations
  
  > **Comments:**
  > **username_1**: Did you try asking on the [help forum](https://groups.google.com/forum/#!forum/genepattern-help)? Or your problem is what is each mutation?  
  > **username_0**: @Llopis: Not yet. I even didn't know about that. I know only GATK forum and this website. I have googled these terms extensively but didn't get even proper definitions. That's why I started the bounty on this question.  
  > **username_2**: CpG transversions are the same as C: G transversions, except that they are followed by a G which means they are potential targets for DNA methylation. Methylcytosine can undergo deamination to Thymine, which makes them mutation hotspots  
  > **username_2**: indel = insertion/deletion. I have no idea what null means in this context  
  > **username_1**: @username_2 Those comments are an answer! With a link to a source you could get the bounty  
  
  ---
  
  ## 0 answers
  
  