Convert VCF file and add covariate information

Question

[asmariyaz23]

Hello

I am new user of PLINK software.

I am trying to convert VCF file to PED format. The sample name in VCF is OPI-10. Here is the command I used:

plink --vcf OPI-10_S8.hap.snp.filtered.mod.vcf.gz \
--recode --out myfile \
--covar pheno_plink.txt \
--covar-number 3

Here is the pheno_plink.txt file for just 1 sample:

OPI-10  OPI-10  50

And here is the PED file generated (truncated):

 OPI10 OPI10 0 0 0 -9 T T T ....

Why is the covariate information not being populated in place of -9? How has OPI-10 become OPI10 in PED file?

Prior to all the modifications I tried, actual sample name in VCF was OPI-10_S8. But I ended up getting OPI10 in first column in PED and S8 in another. Could you help me understand how does PLINK decipher these names?

Thank you for your help in advance.