Identify and avoid calling on extreme high coverage regions. These are found due to mapping problems in repetitive regions and contribute to long run times and errors in variant calling
Avoid low coverage and poor mapping quality annotations when using CallableLoci. These are not used for selecting regions and are better left to the downstream variant caller to annotate
Fixes for detecting excessive coverage: avoid downsampling below mazDepth value, avoid filtering by mapping and reporting low map quality
Ensure that shared excessive coverage regions are removed from final set of callable regions to avoid processing in super deep repetitive regions
Use union of excessive coverage regions for a group to avoid repetitive regions during population calling