text: user6720: I have a .vcf file generated using samtools. I want to know mutations in specific genes by comparing .vcf files with a reference genome. I cannot use the Ensembl VEP tool as my reference genome is not listed there. Can you please help?
  
  user6273: If you want to filter a VCF file, you might want to give VCFtools a try.
  Here is the documentation : VCFtools Manual
  I am not a specialist of this tool but you could do as the following. First build a bedfile with the chromosome names and positions of your genes (start and stop) such as this :
  chr   start   stop   (name)   (score)   (strand)
  
  Then it should work with this command line :
  vcftools --vcf file.vcf --bed positions.bed --out filtered.vcf
  
  The output will be a VCF filtered on the provided regions
  
original_text: 6720: <p>I have a <code>.vcf</code> file generated using <code>samtools</code>. I want to know mutations in specific genes by comparing <code>.vcf</code> files with a reference genome. I cannot use the Ensembl VEP tool as my reference genome is not listed there. Can you please help?</p>
   6273: <p>If you want to filter a VCF file, you might want to give <strong>VCFtools</strong> a try.</p>
  
  <p>Here is the documentation : <a href="http://vcftools.sourceforge.net/man_latest.html" rel="nofollow noreferrer">VCFtools Manual</a></p>
  
  <p>I am not a specialist of this tool but you could do as the following. First build a bedfile with the chromosome names and positions of your genes (start and stop) such as this :</p>
  
  <pre><code>chr   start   stop   (name)   (score)   (strand)
  </code></pre>
  
  <p>Then it should work with this command line :</p>
  
  <pre><code>vcftools --vcf file.vcf --bed positions.bed --out filtered.vcf
  </code></pre>
  
  <p>The output will be a VCF filtered on the provided regions</p>
  