Masking is performed by discarding the masked out nucleotides. As a result the reference is split into separate sequences, which are positioned according to the original unmasked reference sequence.
Note that you should be careful that your data is indeed only sequenced from the target regions. If not, some of the reads that would have matched a masked-out region perfectly may be placed wrongly at another position with a less-perfect match and lead to wrong results for subsequent variant calling. For resequencing purposes, we recommend testing whether masking is appropriate by running the same data set through two rounds of read mapping and variant calling: one with masking and one without. At the end, comparing the results will reveal if any off-target sequences cause problems in the variant calling.
Masking out repeats or using other masks with many regions is not recommended. Repeats are handled well and does not cause any slowdown. On the contrary, masking repeats is likely to cause a dramatic slowdown in speed, increase memory requirements and lead to incorrect read placement.
To mask a reference sequence, first click the Include or Exclude options, and second click the Browse () button to select a track to use for masking.