VG view command hangs with no result (VG Toolkit)
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Entering edit mode
18 months ago
Diomfeas • 0

I'm trying to construct the variation graph as stated in "Working with a whole genome variation graph" in the github wiki of variation graph toolkit and then convert it to gfa for experimental purposes. I manage to create the .vg graph but when i try to convert it to .gfa format with vg view command, an empty gfa file is created and the process just hangs in the terminal with no result. The exact command i use is: vg view human.vg >human.gfa The command used for creating .vg is: vg construct -r ref.fa -v vcf_file.vcf.gz >human.vg Any suggestions on what the problem might be?

vgteam variation graph vg • 521 views
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Entering edit mode
17 months ago
glenn.hickey ▴ 240

The .vg format is very inefficient. Loading a whole-genome .vg file is both slow and very memory-intensive. We have replacement formats that are much better and are working to (transparently) integrate them throughout the vg toolchain, including GFA conversion. In the meantime, your safest bet would be to construct a graph for each chromosome as described here: https://github.com/vgteam/vg/wiki/Working-with-a-whole-genome-variation-graph. You can convert them to GFA individually and concatenate the results.