Answers.Body: <p>Install it via Anaconda/conda.</p>
  <pre><code>conda install -c bioconda vcf2maf 
  conda install -c bioconda/label/cf201901 vcf2maf
  </code></pre>
  <p>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 <a href="https://www.anaconda.com/products/individual" rel="nofollow noreferrer">https://www.anaconda.com/products/individual</a> and just use the either the above and then its done. The conda environments can be considered once vcf2maf is working.</p>
  <p>It is never cool to run Perl on the system command line.</p>
  <hr />
  <p>Once installed ensure the conda activated</p>
  <pre><code>conda activate &lt;env name&gt; # if its base I don't think the &lt;&gt; is needed
  </code></pre>
  <p>Then simply type</p>
  <pre><code>vcf2maf.pl
  </code></pre>
  <p><strong>Output</strong></p>
  <pre><code>&gt; Usage:
  &gt;      perl maf2vcf.pl --help
  &gt;      perl maf2vcf.pl --input-maf test.maf --output-dir vcfs
  </code></pre>
  <p>Its a Perl script hence it will not recognise maf2vcf without the suffix <code>pl</code>. Anaconda doesn't need <code>perl &lt;perlscript&gt;</code>.</p>
  <p>Oh just to mention I just <code>conda install vcf2maf</code> without the channel but I think I've got bioconda on my repo list.</p>
  <hr />
  <p>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 <code>maf2vcf.pl --input-maf test.maf --output-dir vcfs</code> that should work.</p>
  <hr />
  <p><strong>Note of explanation: why Anaconda works</strong></p>
  <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-07T22:00:34.063Z
Answers.Text: Yeah, but how could I use it after it is installed? Running these codes I will only get the outcomes that the package is already installed. However, I could not call vcf2maf in the command line.
Answers.UserDisplayName: Scott XU
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-07T22:14:41.903Z
Answers.Text: Thank you very much for your kind help. I could get the output if I type vcf2maf.pl; however, if I try to use perl vcf2maf.pl --help, I would get an error message: Can't open perl script "vcf2maf.pl": No such file or directory. Do you know why this could happen? Thanks a lot~~~~~
Answers.UserDisplayName: Scott XU
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-07T22:42:26.560Z
Answers.Text: I've just uninstalled .. it was a bit messy.Answered above, anyway its been fun.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-07T21:53:29.867Z
Answers.LastActivityDate: 2022-03-07T22:32:55.917Z
Answers.LastEditDate: 2022-03-07T22:32:55.917Z
Answers.UserDisplayName: M__
Body: <p>I am trying to use a commonly recommended package named <a href="https://github.com/mskcc/vcf2maf" rel="nofollow noreferrer">vcf2maf</a>to convert vcf file to maf file and is reliant on Ensembl's Variant Effect Predictor (VEP) <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4" rel="nofollow noreferrer">here</a>. However, if I follow the guidelines shown on the github, I would get:</p>
  <pre><code>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.
  </code></pre>
  <p>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 <a href="https://gist.github.com/ckandoth/61c65ba96b011f286220fa4832ad2bc0" rel="nofollow noreferrer">gist</a>).</p>
  <p>As a result, I tried to use the <a href="https://anaconda.org/bioconda/vcf2maf" rel="nofollow noreferrer">Conda installation</a> and use the codes:</p>
  <pre><code>conda install -c bioconda vcf2maf
  </code></pre>
  <p>However, after the package was successfully installed, I could not call it in the command line.</p>
  <pre><code>(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
  </code></pre>
  <p>Or, if I want to use the Perl script:
  I will get:</p>
  <pre><code>(base) user-MacBook-Pro:~ user$ perl vcf2maf.pl 
  Can't open Perl script &quot;vcf2maf.pl&quot;: No such file or directory
  </code></pre>
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-07T22:07:05.140Z
Comments.Text: I've just installed it via conda and it works ... I have answered below . Geee wished I'd installed on a custom environment because the uninstallation is a bit messy
Comments.UserDisplayName: M__
Tags: <vcf><maf>
Title: Problems when using vcf2maf
ThreadText: # Problems when using vcf2maf
  
  (Asked by: username_0 on 2022-03-07)
  
  I am trying to use a commonly recommended package named [vcf2maf](https://github.com/mskcc/vcf2maf)to convert vcf file to maf file and is reliant on Ensembl's Variant Effect Predictor (VEP) [here](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4). 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](https://gist.github.com/ckandoth/61c65ba96b011f286220fa4832ad2bc0)).
  
  As a result, I tried to use the [Conda installation](https://anaconda.org/bioconda/vcf2maf) 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:~ username_0$ 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.
  
  **Tags:** vcf, maf
  
  > **Comments:**
  > **username_1**: I've just installed it via conda and it works ... I have answered below . Geee wished I'd installed on a custom environment because the uninstallation is a bit messy  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-03-07. Score: 1 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: Yeah, but how could I use it after it is installed? Running these codes I will only get the outcomes that the package is already installed. However, I could not call vcf2maf in the command line.  
  > **username_0**: Thank you very much for your kind help. I could get the output if I type vcf2maf.pl; however, if I try to use perl vcf2maf.pl --help, I would get an error message: Can't open perl script "vcf2maf.pl": No such file or directory. Do you know why this could happen? Thanks a lot~~~~~  
  > **username_1**: I've just uninstalled .. it was a bit messy.Answered above, anyway its been fun.  
  
  ---
  
  