Hi is there a reason why parabricks uses vg version 1.59 from over a year ago? It has some serious errors that have since been addressed in many releases. For example, if the rescue attempt fails, Giraffe is supposed to consider a read set an alignment even if one read is aligned but the pair is unaligned – the bug in this case made the aligned read also unaligned, and only fixed in vg 1.66.0.
This makes the parabricks container somewhat of its own rabbithole when you have to reconvert everything back to v1.59, including actual pangenome graphs. It would be great if this was addressed.
Cheers,
Sam