I have a series of VCF files (one for each chromosome) that have an incorrect values for the phenotype (all samples have the value "-9"). I have read on other questions that the make-pheno or pheno flags can be used to add phenotype information when creating the PLINK format files. But I am unsure if thsis would work correctly since the VCF files "incorrectly" already provide that information.
plink -- bfile file --make-pheno phenotype_file.phe --make_bed --out out_file
Would this work right even if the VCF files contain the PHENO column? Also how can I generate the phenotype file? Can it be done in a program like Excel and then exported to csv, and then somehow converted to .phe format?
Any help is appreciated!