<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>

CC BY-SA 4.0
2018-07-09T11:39:13.620Z
Did you try asking on the [help forum](https://groups.google.com/forum/#!forum/genepattern-help)? Or your problem is what is each mutation?
llrs
CC BY-SA 4.0
2018-07-09T12:35:23.157Z
@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.
Lot_to_learn
CC BY-SA 4.0
2018-07-10T14:43:55.960Z
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
heathobrien
CC BY-SA 4.0
2018-07-10T14:49:35.197Z
indel = insertion/deletion. I have no idea what null means in this context
heathobrien
CC BY-SA 4.0
2018-07-11T09:03:31.970Z
@heathobrien Those comments are an answer! With a link to a source you could get the bounty
llrs
<genomics><cancer><gatk><mutations>
Meaning of category in MutSigCV
# 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**: @heathobrien Those comments are an answer! With a link to a source you could get the bounty  

---

## 0 answers

