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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?

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  • $\begingroup$ What do you mean by this: “on my system, perl scripts with dependencies are easy to break”? $\endgroup$ – Konrad Rudolph Feb 1 '18 at 13:39
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    $\begingroup$ @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.) $\endgroup$ – ShanZhengYang Feb 1 '18 at 15:32
  • $\begingroup$ 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). $\endgroup$ – Konrad Rudolph Feb 1 '18 at 15:42
  • $\begingroup$ @KonradRudolph I'd agree with that assessment. You're welcome to discuss this with my team. $\endgroup$ – ShanZhengYang Feb 1 '18 at 15:45
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Check this python script vcf2maf.py

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    $\begingroup$ Ironically, from their README: "This code is no longer maintained. Please have a look at: mskcc's vcf2maf." $\endgroup$ – burger Jan 31 '18 at 23:48
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You can use annovar to annotate the vcf, then convert it to maf using the function annovarToMaf of maftools bioconductor package.

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  • $\begingroup$ Can you include links to the tools and packages you refer to. $\endgroup$ – Bioathlete Mar 7 '19 at 16:34

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