Is there any tool that gives SNPs list separately in 2 different populations?

Question

[kc]

Hi all, is there any statistical software that gives SNPs list separately in 2 different population? May be by putting one population as base and comparing the other population with this base And give SNPs list unique in this population but not the base.

Thanks in advance

Answer 1

[Sean Davis]

See the VCFtools manual page here.

[kc]

Thanks Sean!

Answer 2

[Vivek]

Keeping the SNPs from the two populations in two different VCFs and subtracting one from another should likely produce the same result.

[kc]

Hi Vivek,

Thanks for helping! Where can I find this VCF tool?