<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>

CC BY-SA 4.0
2019-03-07T16:34:54.610Z
Can you include links to the tools and packages you refer to.
Bioathlete
CC BY-SA 4.0
2019-03-07T09:09:47.827Z
2019-03-19T10:11:56.000Z
2019-03-19T10:11:56.000Z
mox
<p>Check this python script <a href="https://github.com/cbare/vcf2maf" rel="noreferrer">vcf2maf.py</a></p>

CC BY-SA 3.0
2018-01-31T23:48:54.643Z
Ironically, from their README: "This code is no longer maintained. Please have a look at: mskcc's vcf2maf."
burger
CC BY-SA 3.0
2018-01-31T11:19:26.433Z
2018-01-31T11:19:26.433Z
stack_learner
<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>

CC BY-SA 3.0
2018-02-01T13:39:15.880Z
What do you mean by this: “on my system, perl scripts with dependencies are easy to break”?
Konrad Rudolph
CC BY-SA 3.0
2018-02-01T15:32:09.697Z
@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.)
ShanZhengYang
CC BY-SA 3.0
2018-02-01T15:42:36.103Z
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).
Konrad Rudolph
CC BY-SA 3.0
2018-02-01T15:45:32.897Z
@KonradRudolph I'd agree with that assessment. You're welcome to discuss this with my team.
ShanZhengYang
<vcf><variant-calling><maf>
Tools to do VCF to MAF and MAF to VCF conversion?
# 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**: @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.)  
> **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**: @KonradRudolph 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.  

---

