Question

Variants that are different between the clown and control

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20 months ago

anasjamshed ▴ 140

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 • 701 views

ADD COMMENT • link updated 20 months ago by GenoMax 148k • written 20 months ago by anasjamshed ▴ 140

score 1 · Answer 1 · 2023-05-01

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20 months ago

Pierre Lindenbaum 164k

bctools isec

ADD COMMENT • link 20 months ago by Pierre Lindenbaum 164k

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

ADD REPLY • link 20 months ago by anasjamshed ▴ 140

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

ADD REPLY • link 20 months ago by GenoMax 148k