Fam file information lost on conversation to VCF file

Question

[nick.gold]

Hi,

I am using PLINK 1.9 and am trying to convert a bim, bed, and fam file into VCF format. I use the command

plink --bfile filename --keep-allele-order --recode vcf -- out filename

I then receive the message: 1512 people (184 males, 1319 females, 9 ambiguous) loaded from .fam

I also receive the message: 1503 phenotype values loaded from .fam (this suggests to me that it is successfully reading in my sex and phenotype information into the vcf file)

However, the issue I run into is that when I try to convert the vcf file back into a bim, bed, and fam file using the code below, the fam file ends up having all 0's in the sex column and all -9's in the phenotype column

--vcf filename.vcf --out output_files

Does anyone know why I am losing all my sex and phenotype information when converting my fam file from vcf and back to fam

Answer 1

[4galaxy77]

Because there isn't a natural way for a vcf to store phenotype or sex information - they aren't really designed for that kind of data. It's not present in the vcf, so it can't be present in the resulting fam file.