Tim Millar

Thanks @eric-czech, `decompose_dosages` is a good name. Just a thought, the `call_dosage` variable can optionally be an integer type. So, we could potentially still use it with the `PattersonScaler` and...

Hi @tnguyengel, I'm not familiar INFO/CSQ annotations but you can specify a maximum bound for a VCF field using the `field_defs` parameter. ```python from sgkit.io.vcf import vcf_to_zarr vcf_to_zarr( "example.vcf.gz", "example.zarr",...

@jeromekelleher suggests also adding "Pedigree statistics" top level section to the documentation https://github.com/pystatgen/sgkit/issues/1025#issuecomment-1436755539. > I was actually just looking for documentation this morning answering a question about computing inbreeding from...

This is mostly covered by #1072, but I might leave it open for now as I think there is room for more pedigree specific documentation.

> What do we currently do with plink-like pedigrees Currently we don't offer any pedigree IO, partly because there're a lot of formats! I've opened #1012 to document some generic...

> Or can we not assume anything about paternal/materal ordering in the `parent_id` variable In general no, but the intent was that these can be specified using coordinate when appropriate....

Hi @etnite, thanks for the feedback! That's a good question and something that I need to investigate more thoroughly. In my PhD work I used a similar process to what...

Just an update @etnite, I've released version 0.9.0 which includes a new tool `mchap find-snvs`. This is a very simplistic approach to finding putative SNVs for haplotype assembly but I...

We could also use a sparse equivalent of `GP` if we specify a minimum posterior probability to report. E.g., >= 0.01 would work well with MCMC approximations. Alternatively, we could...

Sorry for the slow response @rfinkers, you can actually get the version with `mchap version`. I'm not sure why I did it a non-standard way, but I'll leave this issue...