Glenn Hickey

Oh boy, I bet this is about me forgetting to set `TOIL_OWNER_TAG`. If it is, I would like to change this issue to a feature request: When I create an...

I'm using 5.6.0 -- that commit almost surely fixes it. Probably the same type of story for #4138 ...

I suspect it's running out of memory when computing snarls. Can you try ``` vg snarls $output/Gh.xg > $output/Gh.snarls ``` then add `-r $output/Gh.snarls` to the `vg call` command line?...

Please follow the [template](https://github.com/vgteam/vg/issues/new?assignees=&labels=&template=report-a-bug.md&title=) when submitting a bug so we have enough information to help you. **1. What were you trying to do?** **2. What did you want to happen?**...

@jltsiren Are "path cover" gbwt's still an option? If so, it'd be possible in theory to index a mingraph for giraffe, then make a vcf with vg call.

Makes sense. Best to use `vg map` instead on minigraph graphs then

> You could try making a graph with Minigraph, or Minigraph and Cactus together, though I don't know if that would scale enough either. @glennhickey might be able to guess....

Two ways to reduce `vg augment`'s memory consumption: * work on PackedGraph format (convert with `vg convert -p` or check the format with `vg stats -F`) * specify a minimum...

`vg deconstruct` gives you all the variants in the graph. `vg call`determines a subset of variants in the graph that are supported by the reads (aka genotyping). If you have...

I will punt this to @jmonlong, who's just gotten this working on our latest graphs. I think `-k 64` is one of the key things.