vg call has very different variant number between xg and hg

Question

[xwwang]

I find that the vg call has a very different number of variants between calling from the xg, xg packed file and hg (hashgraph), hg packed file. How to explain this? Which one is recommended?

command: tested vg version 1.27, 1.29

## For xg mode:
vg pack -x $graph.xg -g $graph.gam  -t 10 -o $graph.gam.pack
vg call -t 10 -m 1,2 $graph.vg  -k $graph.gam.pack  -a >$graph.gam.xg.vcf

## For hg mode:
vg convert $graph.vg -a >$graph.hg
vg pack -x $graph.hg -g $graph.gam -t 10 -o $graph.gam.hg.pack
vg call -t 10 -m 1,2 $graph.hg  -k $graph.gam.hg.pack  -a >$graph.gam.hg.vcf

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Answer 1

[glenn.hickey]

It is important that the same graph be used for both the pack and call commands. In your xg example, you are packing with the xg and calling with the vg. This will produce undefined results. If you pack and call with the same graph, the output should be identical regardless of the format.