The next part of the dialog shown in figure 25.1 lets you mask the reference sequences. Masking refers to a mechanism where parts of the reference sequence are not considered in the mapping. This can be useful for example when mapping data that is captured from specific regions (e.g. for amplicon resequencing). The read mapping will still base its output on the full reference - it is only the core read mapping that ignores regions.
Including or excluding regions (masking)
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.
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. If you have annotations on a sequence instead of a track, you can convert the annotation type to a track (see Converting data to tracks and back).