Dan King

And what, in your expert opinion, should we use for these parameters? Are the singletons important for a dataset like BGE which, I presume, doesn't have many trios? ``` parser.add_argument('--transmitted-singletons',...

@LindoNkambule is the `UNPADDED_INTERVALS` meant to be the calling intervals used to generate the source GVCFs? I'm pretty sure we should be able to get from the PMs the calling...

I just slacked Laura, she mentioned: > The handcurated intervals were optimized for GenotypeGVCFs runtime, so probably not comparable for VQSR runtime I think either generating intervals directly from the...

Don't we usually run VQSR before we've inferred sample relatedness? I don't recall manifest files indicating trios or sib relationships. Is there a usual way for us to deduce that...

Hey @iris-garden ! This was a PR for a new tutorial that our summer intern, Aleisha, worked on during her internship. Could you do a review for me? The goal...

bump @iris-garden

Hey @szarnyasg ! Thanks for the tips! These indeed seem to avoid exceeding the RAM available on my machine. Resident set size appears to peak around 15GiB (I have 32...

I totally understand if this is a WONTFIX / insufficient bandwidth kind of issue. Is there any chance this gets triaged in the next two months? Again, no worries either...

Hey @xuke-hat ! Thanks for investigating! Indeed, this is a ~4,000 by ~8,000 matrix of human genome sequencing data: ``` In [4]: import duckdb ...: duckdb.sql(''' ...: select len(string_split(entries, '^I'))...

Unfortunately, the CI results are private to protect against inadvertent secret leaks. It looks like the docs are failing. The `Locus` should be `hl.Locus`. I suspect the test will pass...