HI All,

Apply vcftools --diff, it is easy to find command/shared variants between two VCF files.

vcftools --vcf  A.vcf --diff B.vcf --diff-site

However, Is there any easy to identify A specific or B specific variants?

Here is what I noticed:

Parameters as interpreted:
        --vcf gnomad.exomes.r2.1.sites.chr21.rec.ExomeStop.vcf
        --diff gnomad.exomes.r2.1.sites.chr21.rec.ExomeStop.vcf.vat
        --diff-site-discordance

After filtering, kept 0 out of 0 Individuals
First Header entry should be #CHROM: #OM
Outputting Discordance By Site...
Found 1696 sites common to both files.
Found 57 sites only in main file.
Found 0 sites only in second file.
After filtering, kept 1753 out of a possible 1753 Sites
Run Time = 0.00 seconds

I want to extract these 57 sites which only belong to main file (the first file)

Thanks.

Sorry. It looks I find the solution:

 awk '$3==1' out.diff.sites | wc -l