Using GATK4 Base Recalibration and VarDict

Quality scores can be adjusted after using Base Recalibration and these changes can be very significant.

This can cause a problem like this: https://github.com/AstraZeneca-NGS/VarDict/issues/61 where no variant was found on the region after adjustment and option -q 15 was needed for variants to appear.

So if you use GATK Base Recalibration, you can check what was changed and adjust parameters for VarDict if needed. Option -p can be helpful in such a case when you run some tests on the region (in the whole run it can be very slow) because it can output variants before filtering and you will see what filters you have to adjust.