Some days ago I did an analysis using VEP (I have filtered by maf<7%), than, I filtered results with a score greater than 0.35 in SIFT and lower than 0.45 in Polyphen, and all works well. I obtained about 148 variants.
Today I would do the same analysis with different filtering (with a lower MAF<5%) but when I would filter results (SIFT <0.35 -PP>0.45...as the previous analysis) it show me only five variants.... now I'm sure I should obtain more variants because of in the previous analysis most of 148 variants have a maf below 5%. Furthermore Sift and PP calculated score just for this 5 variants and not for the other 15.000.
So my question is: is it possible that today, VEP has some bugs or something else?
I also try to filter my variants with maf <80% but I always obtain 5 variants with calculated score