Adding dosage for a SNP as a covariate to a phenotype file

Question

[khn]

Hello

I want to add a SNP information to a phenotype file, in addition to sex, age and PC 1~10. Does anybody know how to do it? I think I need to retrieve dosage information from vcf.gz file first, then retrieve dosage information only for the SNP. Is this how you guys usually do?

Thank you in advance!

Answer 1

[Lemire]

This is something you can do with vcftools. E.g. assuming your dosage is DS:

vcftools --gzvcf vcffile.vcf.gz --extract-FORMAT-info DS \
--snp rs12345 --out outputprefix

and you will get a text file with your dosage information for that particular snp.