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Support faster GBWT #670
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toil-vg is up to date (as far as I can see) with this wiki dating from July: https://github.com/jltsiren/gbwt/wiki/Construction-Benchmarks but couldn't find anything more up to date. @JTSiren Can you please point me to the newer one we should be using? |
The relevant wiki page is https://github.com/vgteam/vg/wiki/Indexing-Huge-Datasets . There are four steps:
This makes building single-chromosome GBWT indexes several times faster than the direct construction. Some issues remain:
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OK Thanks! This should all be do-able in toil-vg, though we'll have to either put the deps/gbwt/ executables into the vg docker image or vg gbwt. I understand that we'll need this for topmed-sized VCFs, but I don't think it's relevant for @cmarkello's 9-days-to-index-the-1kg-graph issue that brought this discussion about. For that, @cmarkello, I think you'll have to post your command line and any changes to the config. I'd suspect lack-of-parallelism due something there rather any problems with the existing GBWT code which does the 1kg graph just fine. |
Make sure toil-vg is using the latest and greatest logic from @jltsiren's wiki
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