Answers.Body: <p>You can use annovar to annotate the vcf, then convert it to maf using the function <code>annovarToMaf</code> of <a href="https://bioconductor.org/packages/release/bioc/html/maftools.html" rel="noreferrer">maftools</a> bioconductor package.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-07T16:34:54.610Z
Answers.Text: Can you include links to the tools and packages you refer to.
Answers.UserDisplayName: Bioathlete
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Answers.CreationDate: 2019-03-07T09:09:47.827Z
Answers.LastActivityDate: 2019-03-19T10:11:56.000Z
Answers.LastEditDate: 2019-03-19T10:11:56.000Z
Answers.UserDisplayName: mox
Answers.Body: <p>Check this python script <a href="https://github.com/cbare/vcf2maf" rel="noreferrer">vcf2maf.py</a></p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-31T23:48:54.643Z
Answers.Text: Ironically, from their README: "This code is no longer maintained. Please have a look at: mskcc's vcf2maf."
Answers.UserDisplayName: burger
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Answers.UserDisplayName: stack_learner
Body: <p>Normally, I would use the <a href="https://github.com/mskcc/vcf2maf" rel="noreferrer">vcf2maf</a> scripts to convert a VCF to a MAF (or vice versa).</p>
  
  <p>This is great software, but on my system, perl scripts with dependencies are easy to break. (Here it uses VEP.)</p>
  
  <p>Are there any other alternatives to this? </p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-01T13:39:15.880Z
Comments.Text: What do you mean by this: “on my system, perl scripts with dependencies are easy to break”?
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-01T15:32:09.697Z
Comments.Text: @KonradRudolph In my experience, perl + bioinformatics dependencies is a nightmare. Our system admin keeps +12 versions of perl to deal with this. (I don't want to start fights with any perlverts, but it is tiresome in contrast to R/Python.)
Comments.UserDisplayName: ShanZhengYang
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-01T15:42:36.103Z
Comments.Text: Interesting, I’m not sure I understand why. At any rate, R definitely has the same, or worse, problem: it fundamentally can’t handle multiple package versions (unlike Python).
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-01T15:45:32.897Z
Comments.Text: @KonradRudolph I'd agree with that assessment. You're welcome to discuss this with my team.
Comments.UserDisplayName: ShanZhengYang
Tags: <vcf><variant-calling><maf>
Title: Tools to do VCF to MAF and MAF to VCF conversion?
ThreadText: # Tools to do VCF to MAF and MAF to VCF conversion?
  
  (Asked by: username_0 on 2018-01-27)
  
  Normally, I would use the [vcf2maf](https://github.com/mskcc/vcf2maf) scripts to convert a VCF to a MAF (or vice versa).
  
  This is great software, but on my system, perl scripts with dependencies are easy to break. (Here it uses VEP.)
  
  Are there any other alternatives to this?
  
  **Tags:** vcf, variant-calling, maf
  
  > **Comments:**
  > **username_1**: What do you mean by this: “on my system, perl scripts with dependencies are easy to break”?  
  > **username_0**: @username_1 In my experience, perl + bioinformatics dependencies is a nightmare. Our system admin keeps +12 versions of perl to deal with this. (I don't want to start fights with any perlverts, but it is tiresome in contrast to R/Python.)  
  > **username_1**: Interesting, I’m not sure I understand why. At any rate, R definitely has the same, or worse, problem: it fundamentally can’t handle multiple package versions (unlike Python).  
  > **username_0**: @username_1 I'd agree with that assessment. You're welcome to discuss this with my team.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_4 on 2018-01-31. Score: 5 | Accepted answer
  
  Check this python script [vcf2maf.py](https://github.com/cbare/vcf2maf)
  
  > **Comments:**
  > **username_5**: Ironically, from their README: "This code is no longer maintained. Please have a look at: mskcc's vcf2maf."  
  
  ---
  
  ### Answer by username_2 on 2019-03-07. Score: 6
  
  You can use annovar to annotate the vcf, then convert it to maf using the function `annovarToMaf` of [maftools](https://bioconductor.org/packages/release/bioc/html/maftools.html) bioconductor package.
  
  > **Comments:**
  > **username_3**: Can you include links to the tools and packages you refer to.  
  
  ---
  
  