Best way to map capture data?

[oiiio]

Does anyone have suggestions for mapping capture data? For example, mapping to the whole genome or mapping to the reference regions within the capture only.

[kmcarr]

Whole genome; always to the whole genome. Remember that all of the target enrichment protocols do just that, the enrich your input set for the target of interest but there will always be off target reads present. You want those off target reads to align to their true location, not be forced into an incorrect alignment because you mapped to an incomplete reference.

[swbarnes2]

Yes, absolutely, whole genome.

Afterwards, you can take a .bed file of your target areas, and use BEDTools to trim the bam so that it only shows you the reads that aligned to target.