I am now confusing about false positive filtering of my called SNVs. I am wondering how do you do the filtering? What tools to use? Should I use two different tools to call and use the SNVs in both calling as the true SNVs? What I used for SNV calling was Varscan2. But my files failed the fpfilter.py as all the variants failed like this:

0 passed filters 194 failed filters 0 failed because no readcounts were returned 35 failed minimim variant count < 3 7 failed minimum variant freq < 0.05 0 failed minimum strandedness < 0.0 194 failed minimum reference readpos < 0.2 194 failed minimum variant readpos < 0.15 194 failed minimum reference dist3 < 0.2 194 failed minimum variant dist3 < 0.15 0 failed maximum reference MMQS > 50 0 failed maximum variant MMQS > 100 0 failed maximum MMQS diff (var - ref) > 50 26 failed maximum mapqual diff (ref - var) > 10 40 failed minimim ref mapqual < 20 55 failed minimim var mapqual < 30 0 failed minimim ref basequal < 15 111 failed minimim var basequal < 30 0 failed maximum RL diff (ref - var) > 0.05