Variants that are different between the clown and control

I have 2 vcf files; one is Clown and the other one is Control. Which tool I can use to find that are different between the 2 samples? vcf-compare -H A.vcf.gz B.vcf.gz will work or not?

difference vcf

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updated 3.3 years ago by GenoMax

• written 3.3 years ago by anasjamshed

1 answer

bctools isec

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written 3.3 years ago by Pierre Lindenbaum

But i think bcftools isec will give common variants , not uncommon?

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written 3.3 years ago by anasjamshed

https://davetang.org/muse/2019/09/02/comparing-vcf-files/

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written 3.3 years ago by GenoMax

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