Problems when using vcf2maf

Question

I am trying to use a commonly recommended package named vcf2mafto convert vcf file to maf file and is reliant on Ensembl's Variant Effect Predictor (VEP) here. However, if I follow the guidelines shown on the github, I would get:

perl vcf2maf.pl --ref-fasta hg38.fa --input-vcf chr21.vcf --output-maf chr21.maf
dyld[33981]: Library not loaded: @rpath/libcrypto.1.0.0.dylib
  Referenced from: /usr/local/anaconda3/bin/samtools
  Reason: tried: '/usr/local/anaconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/anaconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/lib/libcrypto.1.0.0.dylib' (no such file), '/usr/lib/libcrypto.1.0.0.dylib' (no such file)
dyld[33982]: Library not loaded: @rpath/libcrypto.1.0.0.dylib
  Referenced from: /usr/local/anaconda3/bin/samtools
  Reason: tried: '/usr/local/anaconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/anaconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/lib/libcrypto.1.0.0.dylib' (no such file), '/usr/lib/libcrypto.1.0.0.dylib' (no such file)
dyld[33983]: Library not loaded: @rpath/libcrypto.1.0.0.dylib
  Referenced from: /usr/local/anaconda3/bin/samtools
  Reason: tried: '/usr/local/anaconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/anaconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/lib/libcrypto.1.0.0.dylib' (no such file), '/usr/lib/libcrypto.1.0.0.dylib' (no such file)
dyld[33984]: Library not loaded: @rpath/libcrypto.1.0.0.dylib
  Referenced from: /usr/local/anaconda3/bin/samtools
  Reason: tried: '/usr/local/anaconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/anaconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/lib/libcrypto.1.0.0.dylib' (no such file), '/usr/lib/libcrypto.1.0.0.dylib' (no such file)
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 410.

I think the reference is the correct one, and I guess the error might be because of the VEP installation (as I came across a lot of bugs when following their gist).

As a result, I tried to use the Conda installation and use the codes:

conda install -c bioconda vcf2maf

However, after the package was successfully installed, I could not call it in the command line.

(base) user-MacBook-Pro:~ scottxu$ conda install -c bioconda vcf2maf
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

(base) user-MacBook-Pro:~ user$ vcf2maf
-bash: vcf2maf: command not found

Or, if I want to use the Perl script: I will get:

(base) user-MacBook-Pro:~ user$ perl vcf2maf.pl 
Can't open Perl script "vcf2maf.pl": No such file or directory

Could anyone give me suggestions on how to install and use vcf2maf correctly? Thank you very much in advance~~ I am working on macOS Monterey 12.2.1 with an Intel Core i5 processor.

Answer 1

Install it via Anaconda/conda.

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

I personally like Anaconda-navigator for OSX but you would likely go for 'command line version' in part because it will place it in your home directory. Its here https://www.anaconda.com/products/individual and just use the either the above and then its done. The conda environments can be considered once vcf2maf is working.

It is never cool to run Perl on the system command line.

---

Once installed ensure the conda activated

conda activate <env name> # if its base I don't think the <> is needed

Then simply type

vcf2maf.pl

Output

> Usage:
>      perl maf2vcf.pl --help
>      perl maf2vcf.pl --input-maf test.maf --output-dir vcfs

Its a Perl script hence it will not recognise maf2vcf without the suffix pl. Anaconda doesn't need perl <perlscript>.

Oh just to mention I just conda install vcf2maf without the channel but I think I've got bioconda on my repo list.

---

I've just uninstalled it. There appears to be an error with the help docs. The help docs (probably PODs) may not have been uploaded and in any case it will run without them. What conda gives you is the full set of dependencies for the script (makes uninstallation a headache) - however you don't need to worry hence I would just use it maf2vcf.pl --input-maf test.maf --output-dir vcfs that should work.

---

Note of explanation: why Anaconda works

I better explain, the script run by itself is complaining it can't see the dependencies it requires. It doesn't just need them, it needs to see them. Anaconda/conda takes care of all that by downloading the dependencies and ensuring they are all visible. The downside is uninstalling everything afterwards, but that's my problem not the OPs.