How to apply vcftools --diff and extract only the different variants

Question

[eleni.psar]

Hello, I am trying to apply vcftools --diff in order to extract the different variants between two VCF files.

vcftools --vcf marked_IO002_tumor-pe.vcf --diff marked_IO002_normal-pe.vcf --diff-site --out t_v_n

I am getting this as result :

  VCFtools - 0.1.16
    (C) Adam Auton and Anthony Marcketta 2009

    Parameters as interpreted:
            --vcf marked_IO002_tumor-pe.vcf
            --out out.diff.sites
            --diff marked_IO002_normal-pe.vcf
            --diff-site
    Comparing sites in VCF files...
    Found 75584 sites common to both files.
    Found 419593 sites only in main file.
    Found 84102 sites only in second file.
    Found 2908 non-matching overlapping sites.
    After filtering, kept 498085 out of a possible 498085 Sites
    Run Time = 6.00 seconds
    0

I want to extract these 419593 sites which only belong to the main file (the first file) do you know if there is a way to do that? Can these sites that I want to extract be in a new vcf file? If you could help me, I would be more than thankful!

Thanks

[Pierre Lindenbaum]

use bcftools isec

[Pierre Lindenbaum]

and that was the solution suggested in your previous question: How to compare vcf files and keep only their differencies ?

[Pierre Lindenbaum]

cross posted: https://stackoverflow.com/questions/71126377/