Question: update fam file VCF -> plink bfile
0
gravatar for biosigil.blog
2.5 years ago by
biosigil.blog0 wrote:

I have a large VCF (WGS >7000 samples) that I converted to plink bfile with this command

plink --vcf in.vcf --make-bed --out plink

A fam file is produced, but does not reflect the relationships, phenotypes, or genders

I've replaced the fam file with a correct one containing these information. Then I calculate allele frequency with this command

plink --bfile plink --freq counts --out plink

I've noticed that the allele counts are incorrect, like for variant A plink reports an allele count of 1 and when I manually parse the VCF, I find the allele count is 3 (for founders only)

So something went wrong.

How do I convert a VCF into a plink bfile while replacing/updating the fam file, so I don't get these errors.

bfile plink vcf • 1.9k views
ADD COMMENTlink modified 2.5 years ago by chrchang5237.1k • written 2.5 years ago by biosigil.blog0
1
gravatar for chrchang523
2.5 years ago by
chrchang5237.1k
United States
chrchang5237.1k wrote:

--update-parents (http://www.cog-genomics.org/plink/1.9/data#update_indiv ), --update-sex, and --pheno can be used for this purpose.

ADD COMMENTlink written 2.5 years ago by chrchang5237.1k
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