Using PLINK to filter VCF files

1

Hello,

I am trying to filter a VCF file based on the R2 value that each SNP has. I would like to only keep the entries which have a R2 >= 0.3.

Are these the right commands/procedure?

plink --vcf dataset.dose.vcf ----recode --out dataset.dose #(vcf to map/ped)

plink --file dataset.dose  --indep-pairwise  1345835 5 0.3 --out dataset.dose #(to get a list of SNPs R2 >= 0.3)

plink --file dataset.dose --extract plink.prune.in --make-bed --out pruneddata #(to perform the extraction of the SNPs and convert map/ped files to bed/bim/fam)

Diego


GWAS


PLINK


vcf

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