Jonathon LeFaive

Thanks. Can you describe the MD field? The only dependencies needed to build the sav CLI are libzstd, libz, and shrinkwrap (https://github.com/jonathonl/shrinkwrap/archive/395361020c84f664d50c1ec51055e107d9178ad3.tar.gz). Shrinkwrap is a header-only library. The other two...

Great. I think `--pbwt-fields AD,MD,DP,GQ,PL` should work well. Any fields that compress well with your delta encoding "should" benefit from PBWT. Your delta encoding will be faster to [de]serialize though,...

Ok. If MD is mostly zero, then `--sparse-fields GT,MD --pbwt-fields AD,DP,GQ,PL` will probably work best.

Hmm... there's no application logic that I can think of that would explain this. I have a 200k data set that I can use to try to reproduce. Are your...

See point 4 in https://github.com/statgen/libStatGen/issues/20#issuecomment-425575055.

I'm surprised that DosageConverter doesn't support HDS fields (which is now the default format field for Minimac v4.1), but you can get around this by adding `-f DS` to your...

Can you elaborate on the use case for your downstream analysis. This information is redundant with what is already in the VCF records. Note: Minimac v4.1 uses the ID column...

I forked DosageCoverter and made a fix for plink conversions. Please try https://github.com/jonathonl/DosageConvertor. If this works for you, I will create a pull request in the main repo.

I'm very skeptical that Minimac4.1 is changing the reference allele. If this is happening, it is likely happening somewhere else in your pipeline. But if you can provide an example,...

Ok, I will check this out sometime this week.