giraffe alignment for exome sequencing

Question

[Michal Frenkel]

Is there a way to restrict alignment to exome regions only? When I use normal alignment (./vg giraffe -p -Z "$gbz_file" -m "$min_file" -d "$dist_file" -f "$file1" -f "$file2" > "$output_filename" .) on vg version v1.50.1, I get a lot of single reads mapped to non-exome regions. I also get very long variants that include both exome and non-exome regions that I don't know how to interpret in light to the fact that it is only based on exome reads.
Any help in understanding this ?