Question: Extracting A Rs* Genotype Using Vcf Tools
1
gravatar for Curiosity
9.2 years ago by
Curiosity120
Curiosity120 wrote:

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

gatk • 3.3k views
ADD COMMENTlink written 9.2 years ago by Curiosity120

what is gatk? Did you mean gawk?

ADD REPLYlink written 9.1 years ago by Giovanni M Dall'Olio27k
2
gravatar for Adam
9.2 years ago by
Adam1.0k
United States
Adam1.0k wrote:

I think you want:

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

ADD COMMENTlink modified 9.2 years ago • written 9.2 years ago by Adam1.0k
1
gravatar for lh3
9.2 years ago by
lh332k
United States
lh332k wrote:

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

ADD COMMENTlink written 9.2 years ago by lh332k
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