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