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frankvogt / vcf2gwas

Python API for comprehensive GWAS analysis using GEMMA
GNU General Public License v3.0
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Multivariate Analysis #17

Closed M-Ingold closed 1 year ago

M-Ingold commented 1 year ago

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

frankvogt commented 1 year ago

Hi Markus, There is indeed a bug in vcf2gwas, thanks for pointing it out! It will be fixed in the next update. Cheers, Frank

frankvogt commented 1 year ago

From v0.8.8 onwards the bug is fixed and multivariate analysis works as intended.