I’m using vg giraffe with the HPRC pangenome graph and was wondering if it’s possible to align reads to only a subset of the graph (for example, a single chromosome or a specific region), similar to how you can align to one chromosome with a linear reference. If this is possible:

• how is subsetting and more importantly indexing usually handled?
• are there important limitations or downsides to doing this (accuracy, missing context)?

My interest is not just for testing, but also to understand whether this can make sense for targeted analyses or when resources are limited. Thanks!