How do different enrichment methods for sequencing affect analysis/computation decisions?

[cansavvy]

I haven't been able to find this answer anywhere yet. But I'd like to know for WXS and Targeted sequencing methods, what pitfalls or other aspects of the data analysis should a person be aware of based on the enrichment method that was done?

Aka how should the analysis change if hybridzation capture vs amplicon enrichment were used? Has anyone done a side by side comparison? Do any tools out there have settings that account for differences between enrichment methods?