I ran freebayes and vardict using the same sample and saw that the QUAL for both callers are very different. The variant below are the false-positive variants. Freebayes suggests do filtering using QUAL > 20; but it won't work for vardict since the QUAL for these variants are high.
Does anyone know why QUAL for these callers are so different? How should one filter for variants if Vardict was used? Thanks for the help!