The 'Reference masking' filters allow the user to only perform variant calling (including error model estimation) in specific regions. In addition to selecting an annotation track, there are two parameters to specify:
- Ignore positions with coverage above: All positions with coverage above this value will be ignored when inspecting the read mapping for variants. The option is highly useful in cases where you have a read mapping which has areas of extremely high coverage as are areas around centromeres in whole genome sequencing applications for example.
- Restrict calling to target regions: Only positions in the regions specified will be inspected for variants.