Setting Reference Genome

[KarthickRajaNarayanan]

I have a doubt on this step in Population stratification. I can understand why we are changing the reference alleles based on the reference data set. But is it okay to do that? Because, we are generating vcf files based on a reference genome (ex: GRCh37) and the 1000 genome data set is made up based on GRCh38. So I'm changing the reference alleles based on 1000 genome data set. What is the point in generating vcf files using our preferred reference genome? We could have created vcf files using the other reference genome initially itself. But why we are not doing that? Please resolve my doubt.

Thanks