Entering edit mode
16 months ago
Nai
▴
50
I have vcf file which belongs to cases only. I have to calculate frequencies and pvalue and odds ratio. It showed note: NO phenotypes present. I used flags --allow-no-sex --no-FID
Kindly help me to get-rid off.
You can't calculate p-value or odds ratio if you only have cases (assuming you are analysing a binary case control trait?)
No...I have GWAS vcf file only with genotype information
OK well if you only have cases then you cannot calculate an pvalue. Is this for a school project or something?
Thank you. Its dissertation project. I have only GWAS with cases