phenofile.txt and my.phenotype in PLINK/SEQ

Question

[Randel]

I cannot find templates for phenofile.txt and my.phenotype in the following PLINK/SEQ code. Can anyone provide the link to the templates? For phenofile.txt, is it like the file here? Can I just have two columns, ID and phenotype? Thanks!

pseq data.vcf.gz v-assoc --phenotype phenofile.txt my.phenotype

Answer 1

[Randel]

The example is like below. You need to load phenotype to your project first.

pseq proj load-pheno --file myphe.phe
pseq proj v-assoc --phenotype myphe > output.txt

The file myphe.phe begins with

##myphe
#ID    myphe
1    1
2    0
3    1