text: user146: Normally, I would use the 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? 
  
  user1377: Check this python script vcf2maf.py
  
  user3772: You can use annovar to annotate the vcf, then convert it to maf using the function annovarToMaf of maftools bioconductor package.
  
original_text: 146: <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>
   1377: <p>Check this python script <a href="https://github.com/cbare/vcf2maf" rel="noreferrer">vcf2maf.py</a></p>
   3772: <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="nofollow noreferrer">maftools</a> bioconductor package.</p>
  