Can't view Manhattan and QQ-plots

[TinaNeik339]

Hi,

May I ask how come I can't view any Manhattan and QQ plots using the code below?

(myenv) tinaneik@Tinas-MacBook-Pro-2 vcf2gwas % vcf2gwas -v ~/Downloads/group1B.vcf -pf ~/Downloads/Phenotype1B.csv -ap -lmm -nl -q 0.05 -KC 0.5 -sv 0 -sd -P 3 -fs 26 -o Output

I can only view the log files under Output folder -> Linear_Mixed_Model folder, for example one of the log files shows this:

**
Beginning with analysis of Phenotype1B_pca.part1.csv

Preparing files

Checking and adjusting files..
Checking individuals in VCF file..
Checking individuals in phenotype file..
All phenotype and genotype individuals match
Removed 0 out of 104 genotype individuals, 104 remaining
Removed 0 out of 104 phenotype individuals, 104 remaining
No covariate file specified
In total, removed 0 out of 104 genotype individuals, 104 remaining
Files successfully adjusted

Filtering and converting files

Converting to PLINK BED..
Successfully converted to PLINK BED (Duration: 1.5 seconds)

Performing principal component analysis..

**

Appreciate your help.

Thank you.