text: user3124: I know that I can use bcftools isec to compare two VCF files containing single nucleotide variants (SNVs); it will generate four possible output files: one with all of the unique called SNVs in file 1, one with all of the unique called SNVs in file 2, one with all of the SNVs from file 1 that were also found in file 2, and finally one with all of the SNVs from file 2 that were also found in file 1.  
  Is there a similar type of tool that will allow one to compare structural variants (SVs) between two VCF files?  I am about to tweak one of my Perl scripts (that currently uses the VCF.pm Perl module to parse VCF files) to perform this calculation (because thus far I have not found any tools designed for SVs) but I thought I would ask in this forum in case anyone else has already invented this wheel.
  
  user3732: The tool that you want to use for this task is bedtools window.
  
original_text: 3124: <p>I know that I can use <code>bcftools isec</code> to compare two VCF files containing single nucleotide variants (SNVs); it will generate four possible output files: one with all of the unique called SNVs in file 1, one with all of the unique called SNVs in file 2, one with all of the SNVs from file 1 that were also found in file 2, and finally one with all of the SNVs from file 2 that were also found in file 1.  </p>
  
  <p>Is there a similar type of tool that will allow one to compare structural variants (SVs) between two VCF files?  I am about to tweak one of my Perl scripts (that currently uses the VCF.pm Perl module to parse VCF files) to perform this calculation (because thus far I have not found any tools designed for SVs) but I thought I would ask in this forum in case anyone else has already invented this wheel.</p>
   3732: <p>The tool that you want to use for this task is <code>bedtools window</code>.</p>
  