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Scalable genetics toolkit
There is a new plan to bring Zarr up to date with the V3 spec over the next few months (see https://github.com/zarr-developers/zarr-python/discussions/1480). This issue is to run sgkit tests against...
There doesn't seem to be any link between variables, and how they are computed either in the documentation, or in error messages. For example, I want to get ``variant_allele_frequency`` which...
This is currently only implemented for the diploid biallelic case. Generalizing it to the multiallelic case would require that the number of possible alleles at each variant is known. See...
Hi there, I'm playing around with PC-Relate estimation. I'm using the malariagen_data package to load some data, then using sgkit to remove multiallelic/singleton/invariant/nonsegregating sites, perform a PCA, and run PC-Relate....
Can you tell me can I import individual sample vcfs, 100k and more?
The `write_vcf` function doesn't support float64 which makes sense given it's not supported by the VCF specification. However, manually converting float64 arrays to float32 is a bit of a pain,...
hi @all I have a VCF with three populations. I use sg.pbs to calculate pbs. I got the pbs values, but I want to get CHROM BIN_START BIN_END PBS four...
We often have the use case of comparing two or more datasets where the corresponding sites have different allele mappings. For example, the ordering could be different, or one dataset...
We don't currently have any IO functionality for pedigree formats. These are usually tabular but can be quite variable. We should document how to read in some generic examples and...
I was looking over our [contributing guide](https://pystatgen.github.io/sgkit/latest/contributing.html) while setting up another project and realized we are not yet using [Ruff](https://github.com/charliermarsh/ruff). I think we can replace Black, Flake8, and isort with...
