I am looking to generate a list of SNPs that are unique to different samples.
To that end, I used bcftools to generate a list of common SNPs for each sample as follows:
# for 9 samples bcftools isec -p intersection -n =9 *vcf.gz
Now I am trying to subtract the common SNPs from the original VCF files to get the SNPs that are unique to each sample. I assume this should also be possible using bcftools but I could not find a "subtract" command.
Any advice is appreciated!