how to extract unique snps in a vcf file by comparing with multiple vcf files

Question

[nikhil]

how to extract unique snps in a vcf file by comparing with multiple vcf files and make a file with unique snps

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EDIT by Ram

OP created anotehr post a couple of hours later with this information:

I want to extract unique SNPs in a single vcf file (IA.vcf.gz) compared with other 19 vcf files by following the command

bcftools isec -c snps -C IA.vcf.gz 502.vcf.gz 505.vcf.gz 90G.vcf.gz 91B.vcf.gz 93K.vcf.gz 93L.vcf.gz 98M.vcf.gz DM.vcf.gz Dw.vcf.gz IA.vcf.gz LE.vcf.gz MT.vcf.gz P10.vcf.gz PI34vcf.gz PI.vcf.gz PI3.vcf.gz PL.vcf.gz PLYGma-PI.vcf.gz R2.vcf.gz R.vcf.gz -p new100IACunique

Am I doing it right?

Thanks

Answer 1

[Pierre Lindenbaum]

use bcftools isec

[nikhil]

thank you, bcftools isec is working well.

[Pierre Lindenbaum]

so validate the answer to close the question please (Green tick on the left).