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I tried to install vcf2maf following this tutorial from GitHub: https://github.com/mskcc/vcf2maf.

I get a repeat error when I try to test out vcf2maf using the code:

perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf

The error message looks like this:

'''STATUS: Running VEP and writing to: tests/test.vep.vcf
ERROR: Cannot find VEP script under: /Users/user/miniconda3/bin'''

Basically I followed every steps provided on the tutorial. Does anyone could help me find out what is going wrong?

I am working on macOS Monterey 12.2.1 with an Intel Core i5 processor.

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  • $\begingroup$ Could you kindly provide details of your hardware and system? $\endgroup$
    – M__ ♦
    Feb 14, 2022 at 20:28
  • $\begingroup$ I have the same problem. I tried conda installation as indicated, however, the error is not solved. Perl version is v5.36.0. $\endgroup$
    – user15601
    Jun 9, 2022 at 2:06

1 Answer 1

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Install it via anaconda/conda either,

conda install -c bioconda vcf2maf
conda install -c bioconda/label/cf201901 vcf2maf

I would be surprised if that installation fails. A possible issue is Perl version and system version.

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  • $\begingroup$ Thanks! I think that works! $\endgroup$
    – Scott XU
    Feb 14, 2022 at 20:34
  • $\begingroup$ Cool, please remember to 'accept' and if possible upvote $\endgroup$
    – M__ ♦
    Feb 14, 2022 at 20:46

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