The 'Reference masking' filters allow the user to only perform variant calling (incl. error model estimation) in specific regions. There are two parameters to specify this:
- Ignore positions with coverage above: All positions with coverage above this value will be ignored when inspecting the read mapping for variants.
- Restrict calling to target regions: Only positions in the regions specified will be inspected for variants.
Note that when the option
Ignore positions with coverage above is chosen, any position with coverage above the specified value will be ignored by the algorithm, and no variants will be called at these positions. The option is highly useful in cases where you have a read mapping which has areas of extremely high coverage, that you are not really interested in. An example is areas around centromeres in whole genome sequencing applications. The computational requirements may be prohibitive if you consider the full read mapping, but manageable if you exclude the (un-interesting) high-coverage areas.
Also note that the Restrict calling to target regions parameter is optional. When not specified, the full read mapping will be examined.
