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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.

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  • $\begingroup$ It looks like no one has answered yet. Maybe others would find it easier to help you out if you provided a minimal example of the VCF files that you are trying to compare? $\endgroup$
    – winni2k
    Commented Nov 25, 2018 at 14:11

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The tool that you want to use for this task is bedtools window.

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