Question: vg call has very different variant number between xg and hg
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xwwang • 20 wrote:
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
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modified 8 weeks ago
by
glenn.hickey • 220
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written
11 weeks ago by
xwwang • 20
Please use the formatting bar (especially the
codeoption) to present your post better. You can use backticks for inline code (`text` becomestext), 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.