File with rsid and genotype based on rsid list and WGS files (.bam, snp.vcf.gz...)

Question

[Marta]

Hi,

I have a txt file (let's call it positions.txt) with a list of SNPs (rs id's only). Based on WGS files, I would like to prepare a file with genotypes for these positions with two columns - rsid and genotype for it. Rsid would be from positions.txt and genotype from WGS files.

I want to upload this file to MTHFR genetics UK for their report.

Can someone help with the best tools and commands?

Kind regards,

Marta