no SNPs in common between prior studies and the conventional GWAS

[Xuemin-Wang]

Dear author,

Another issue came along as I was using bGWAS (as in the title and below). I have checked the two ZMatrices files manually. There are large amount of SNPs in common among the gwas studies.

Adding data from the conventional GWAS :

"allEC_unmunged" Done! 0 SNPs in common between prior studies and the conventional GWAS

Thresholding...

0 SNPs left after thresholding breast cancer - Age of Menarche - PCOS - uterine fibroids - epithelial ovarian cancer - T2D - HDL cholesterol - hypertension - Pulse wave Arterial Stiffness index - Impedance of whole body - High light scatter retic ulocyte percentage - Creatinine (enzymatic) in urine - Alanine aminotransferase (U/L) - C-reactive protein (mg/L) - SHBG (nmol/L) - Ankle spacing width - Length of menstrual cycle - Vascular/heart problems diagnosed by doctor: Heart attack : removed (less than 2 instrument after thresholding) 0 studies left after thresholding Pruning MR instruments... distance : 500Kb

Then it stayed in this status for hours without progressing.

I read the original code, but didn't find a clue.

Do you have any idea what's going on?

Regards, xuemin