Question: update fam file VCF -> plink bfile
0
biosigil.blog • 0 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.
ADD COMMENT
• link
•
modified 17 months ago
by
chrchang523 ♦ 5.4k
•
written
17 months ago by
biosigil.blog • 0
