Using a phenotype file with several phenotype columns- PLINK2

Question

[haasroni]

Hi all,

I have created a tsv file ( phenotypes.tsv ) that includes phenotypes that I am using for a plink command with the --phenom flag. The first column is the #IID col with sample names that match the names in my vcf file (with genotypes). The other columns are phenotypes.

For example, the phenotypes.tsv file potentially looks like that:

 #IID    phenotype_1    phenotype_2        phenotype_3       phenotype_4      phenotype_5

individual1     223       30   10    4       K1

When I run this command to generate bed bim and fam plink files:

plink2 --vcf genotypes.vcf --make-bed --allow-extra-chr --max-alleles 2 --pheno phenotypes.tsv

It says (as I would expect)

5 phenotypes loaded (4 quantitative, 1 categorical).

But in the fam file, I only see that phenotype_1 column with the exact values presented in it, e.g.

0       individual1    0       0       0      223

It seems that the other phenotypes aren't taken into account.

Could anyone help me understand why is it?

Thank you!

Answer 1

[chrchang523]

The .fam format allows for only one phenotype column. Use --pfile/--make-pgen instead of --bfile/--make-bed if you want to embed more.

[haasroni]

Thank you very much!