Doesn't GraphAligner support `.vg` graph?

[tanger-code]

When I use .vg graph in GraphAligner's mapping command GraphAligner -g chr21.vg -f chr21.fq -t 88 -a graphaligner_aln.gam -x vg, there is something error: Why did I get this error？Doesn't GraphAligner support .vg graph?

[tanger-code]

When I use the GFA graph, it works. But why can't it be vg graph?

[maickrau]

It's supposed to support vg graph. Could you please upload the graph?

[tanger-code]

https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-grch38/hprc-v1.1-mc-grch38.chroms/chr21.vg

[maickrau]

This seems to be caused by changes in the vg file format. Up until vg version 1.40.0 the default was the protobuf format which GraphAligner can read, and then it was changed to a PackedGraph format which GraphAligner does not read, while keeping the same file extension .vg for both different formats. You can check the file format with vg stats -F chr21.vg which reports that the graph is indeed in PackedGraph format instead of protobuf.

You can sidestep this issue either by using the GFA graph, or by using vg to convert the graph from PackedGraph to protobuf. I'll leave this issue open while I think about a solution.

[yeeus]

@maickrau hi, have you solved this problem? I also met this issue