Question

Variants that are different between the clown and control

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12 months ago

anasjamshed ▴ 120

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 • 521 views

ADD COMMENT • link updated 12 months ago by GenoMax 141k • written 12 months ago by anasjamshed ▴ 120

score 1 · Answer 1 · 2023-05-01

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12 months ago

Pierre Lindenbaum 161k

bctools isec

ADD COMMENT • link 12 months ago by Pierre Lindenbaum 161k

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

ADD REPLY • link 12 months ago by anasjamshed ▴ 120

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

ADD REPLY • link 12 months ago by GenoMax 141k