R or Python packages to work with SNPs

Question

[schlogl]

Hi guys hope everyone save and well.

I would like to know if you guys could me help pointing out some packages (R/python/or a software)to work with snps from 1000Genomes or esembl?

Need to get for example, some specific snps from south american pop, for do other analysis.

Thanks.

Paulo

[4galaxy77]

I know it's not in Python or R, but bcftools is probably your best bet if you want to just pick out the genotypes from a big .vcf, its probably the most memory efficient and quickest option.

Answer 1

[aays]

I don't know much about the R side, but cyvcf2 is your best bet for processing VCFs in Python - fast and efficient. Here's the GitHub repo and here's the documentation.