BAM creation - vg surject vs vg mpmap output

Question

[AshleeThomson]

I have a graph that I am mapping RNA seq reads to and I want to create a BAM for a comparison study. Is there any difference between using vg surject, and selecting BAM as the output format when using vg mpmap. I've created both GAMP and BAM following mpmap with no issues, but was just curious if I should be using surject instead.

Answer 1

[Rachel]

From what I understand, there is indeed a difference. vg surject recomputes the alignment produced with the reference used to build the graph. In other words it realigns the alignment, with the original linear reference.