Construct a pangenome for a specific region of a chromosome

[HY6Wu]

Hello,
Thank you for developing such a valuable tool!
I am currently preparing to use the Minigraph-Cactus Pangenome Pipeline to construct a pangenome for a specific region of a chromosome. The reference I'm using is a segment of the chromosome, approximately 1 million base pairs in length. I would like to inquire whether the other genomes I input also need to be trimmed to the corresponding region before further constructing the pangenome more effectively? If not trimmed (some input genomes have significant length differences compared to the reference), I've noticed that they tend to be discarded.
Additionally, is it possible to use the VCF result files from the constructed pangenome to build a phylogenetic tree? I would greatly appreciate any suggestions you might have!

[glennhickey]

If at all possible, it's generally better to do the whole chromosome, then extract the subgraph you want after. Otherwise it's best to trim all the genomes. And failing that you may be able to get a graph using --permissiveContigFilger 0