Adjust hard filtering filters - HIGH PRIORITY

[LysianeBouchard]

Description of feature

We will need to tweak the filters used in the hard filtering process as we are not sure that they are optimal.

Look at the recommendations in this article:
https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering

These parameters should be documented properly as well as the rationale for the choice of default values.