Removing common SNPs from a set of VCF files
Hi all,
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!
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