How to change the output reference for vg giraffe BAM output

Question

[idiaz026]

I constructed a pan genome graph with mingraph cactus with two reference genomes specified. I am trying to align reads to the graph and produce a BAM file that is specific to one of the references. How can I specify which reference is used during the surjection to the output BAM?

Answer 1

[glenn.hickey]

You need to use this options in vg giraffe

--ref-paths FILE              ordered list of paths in the graph, one per line or HTSlib .dict, for HTSLib @SQ headers

You can see the paths in your graph with vg paths -Lv <graph>.gbz. When specifying the ref paths, you don't need to worry about suffixes like [32333-4444444].