Extracting A Rs* Genotype Using Vcf Tools

Question

[Curiosity]

Does any one know how to extract a SNP genotype from 1000 Genome data easily? VCF tools of GATK?

[Giovanni M Dall'Olio]

what is gatk? Did you mean gawk?

Answer 1

[Adam]

I think you want:

vcftools --vcf vcf_file --snp rs_id --recode --keep-INFO-all --out output_prefix

Answer 2

[lh3]

awk '/^#/||$2=="rs123456"' in.vcf > out.vcf