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)
Sorry. It looks I find the solution:
awk '$3==1' out.diff.sites | wc -l