How to subset a multisample VCF file for performing selection scan analysis?

Question

[anikcropscience]

Hello,

I have a multisample vcf file comprising 99 individuals from 11 populations. As the reference genome is only scaffolded (not developed to a chromosome scale yet), the VCF file contains SNPs that are distributed over ~200 scaffolds. I want to perform selection scan analyses using different tools like SweeD, LASSI-Plus, SelScan etc. However, most of these selection scan tools require the vcf file to split into the individual chromosome, which I cannot do currently.

Is it possible to subset a vcf into a group of Scaffolds and then run these tools? If not, can you please suggest how can I carry on with the analyses here? Because running a selection scan on ~200 scaffolds seems unreasonable since some of the scaffolds contain only a few SNPs.

Thank you

[Pierre Lindenbaum]

to split into the individual chromosome, which I cannot do currently.

what is the difference between a chromosome and a scaffold here ?

[anikcropscience]

The organism has 12 chromosomes and my reference genome is scaffolded with Hi-C data that produced ~200 of them. They are not anchored to the chromosome.