Removing common SNPs from a set of VCF files

Question

[Lina F]

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!

Answer 1

[ATpoint]

Have a look at the --complement option within isec. It prints all entries but the ones that you supply in B.

[Lina F]

Great, thanks for pointing me in the right direction!