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

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!

snp genome gene
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updated by Lemire Lemire • written by khn khn

1 answer

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.

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written by Lemire Lemire

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