Jordan Eizenga

Try using `vg find -p 1:10000000-10001000 -x 1.xg -c 2` to extract the graph before visualizing it.

Neither the `-c` graph nor the non-`-c` graph is incorrect. They're just different queries. When you query the graph without `-c`, you get *only* the nodes of the path itself....

`vg pack` doesn't retain that information in the `.pack` file. If you want to query specific reads by node ID, you can use `vg gamsort` to create a `.gai` index...

Okay, I'll package that up with the PR for the algorithm I'm writing.

FWIW, the spec does indeed say [here](https://github.com/pangenome/PanSN-spec#the-pattern) that haplotype ID is a number.

Closing this issue because I believe we worked it out over email.

I vaguely recall that GraphAligner might not be able to output mapping qualities. It would be worth checking me on this though.

I think the right approach would be to modify the ref allele in the VCF to match the reference. Modifying the reference itself will change the coordinate system, which will...

> Liftover BAM file is not recommended especially for applications like variant calling, since it is relatively easy to re-align the reads (extracted from the original BAM file). Generally, I...

To use the tools in the VG toolkit, you would need either genome assemblies or variant calls for the inbred lines. Do you have that available?