Faith Okamoto

Something you could do to debug is r-run giraffe with `--track-provenance` and then use `scripts/giraffe-facts.py` with its `--track last any` option. This will make a table showing how many reads...

Oh, I think those improvements were in the [v1.66 version](https://github.com/vgteam/vg/releases/tag/v1.66.0) of giraffe-facts. You might want to pull the most recent script from the vg repository. It's not part of the...

@adamnovak help, why would reads be failing to get any hits? (I haven't tried to fix this problem before and I'm about to leave on vacation.)

Oh, hey, I actually put "find minimizers in this sequence" and "query index for the count of this minimizer" in something command-line accessible. Specifically, use `vg cluster --hit-cap 0 --hits-above...

That directory seems to have scripts. With READMEs too. For example, in the `human/toil-scripts` there is [`map.sh`](https://github.com/vgteam/sv-genotyping-paper/blob/master/human/toil-scripts/map.sh). What specifically else are you looking for? Also, I'm not sure what "essay"...

I think this section from the Methods explains what "non-repeat" means in this context: > We also explored the performance of vg and SMRT-SV v2 Genotyper in different sets of...

whoops somehow closed this while I was trying to type my previous comment

What command did you run, and what data did you use?

Yeah, I'm pretty sure that we name the transcript paths by the names in the GTF files, so having duplicate names is an issue. Possible fix would be to have...

Of course that prefixing could also be done by the user outside of vg, which is probably better?