text: user180: Is there a vcf file on the GRCh38 assembly with common cancer mutations I can download somewhere? Maybe from one of the big international cancer genomics consortia?
  By common, I mean whichever mutations have been found recurrent in different types of cancer. 
  
  user73: The trouble with looking for cancer-associated variants is that it can be difficult to tease out spurious effects (e.g. ethnicity) from causative variants. If you're interested in what genes are implicated in most types of cancer, the annotations for the NanoString panels are quite good:
  
  cancer pathways
  cancer progression
  
  The "Support documents" section of those pages has a link to an Excel file with gene lists and probe sequences. While these lists don't give information about variants that disrupt function, I'm struggling a bit to think through why it would be useful in advance to know that, unless the aim is to induce cancer through CRISPR or something like that.
  
  user298: Your question doesn't give enough information for a specific answer but this should do for a start.
  
  Get the VCF file describing all variants in Clinvar from NCBI:
  wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
  
  Extract any variants whose VCF line contains the word "cancer":
  zgrep -iE '^#|CLNDBN=[^;]*cancer' clinvar.vcf.gz > cancer.vcf
  
  
  Now, you should probably filter that further based on variant frequency, type of cancer, etc etc but that should be a good start. 
  
  user35: If you are looking for cancer mutations, the primary resource is COSMIC and they provide GRCh38 VCFs. The download page is here: http://cancer.sanger.ac.uk/cosmic/download
  It'll be up to you how you define "common", but the VCF includes a lot of information you can use.
  
original_text: 180: <p>Is there a vcf file on the GRCh38 assembly with common cancer mutations I can download somewhere? Maybe from one of the big international cancer genomics consortia?</p>
  
  <p>By common, I mean whichever mutations have been found recurrent in different types of cancer. </p>
   73: <p>The trouble with looking for cancer-associated variants is that it can be difficult to tease out spurious effects (e.g. ethnicity) from causative variants. If you're interested in what <em>genes</em> are implicated in most types of cancer, the annotations for the NanoString panels are quite good:</p>
  
  <ul>
  <li><a href="https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel" rel="nofollow noreferrer">cancer pathways</a></li>
  <li><a href="https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-progression-panel" rel="nofollow noreferrer">cancer progression</a></li>
  </ul>
  
  <p>The "Support documents" section of those pages has a link to an Excel file with gene lists and probe sequences. While these lists don't give information about variants that disrupt function, I'm struggling a bit to think through why it would be useful in advance to know that, unless the aim is to induce cancer through CRISPR or something like that.</p>
   298: <p>Your question doesn't give enough information for a specific answer but this should do for a start.</p>
  
  <ol>
  <li><p>Get the VCF file describing all variants in Clinvar from NCBI:</p>
  
  <pre><code>wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
  </code></pre></li>
  <li><p>Extract any variants whose VCF line contains the word "cancer":</p>
  
  <pre><code>zgrep -iE '^#|CLNDBN=[^;]*cancer' clinvar.vcf.gz &gt; cancer.vcf
  </code></pre></li>
  </ol>
  
  <p>Now, you should probably filter that further based on variant frequency, type of cancer, etc etc but that should be a good start. </p>
   35: <p>If you are looking for cancer mutations, the primary resource is COSMIC and they provide GRCh38 VCFs. The download page is here: <a href="http://cancer.sanger.ac.uk/cosmic/download" rel="noreferrer">http://cancer.sanger.ac.uk/cosmic/download</a></p>
  
  <p>It'll be up to you how you define "common", but the VCF includes a lot of information you can use.</p>
  