This tool is very convenient for running multiple univariate analyses! However, when I tried to run a multivariate analysis, the program only uses the first of my four phenotypes with the following input, running in univariate mode:
vcf2gwas -v input.vcf -lmm --multi -pf phenotypes.csv -k kinship.txt -ap -T 36
I tried using the -m instead of the --multi flag, and also -p 1 -p2 -p3 -p4 instead of -ap.
Could this be a problem with my input or with vcf2gwas?
Hello,
This tool is very convenient for running multiple univariate analyses! However, when I tried to run a multivariate analysis, the program only uses the first of my four phenotypes with the following input, running in univariate mode: vcf2gwas -v input.vcf -lmm --multi -pf phenotypes.csv -k kinship.txt -ap -T 36
I tried using the -m instead of the --multi flag, and also -p 1 -p2 -p3 -p4 instead of -ap.
Could this be a problem with my input or with vcf2gwas?
Thank you, Markus