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Requirements for UKB GWAS
See original GitHub issueTo run a basic GWAS on UKB data, here are some of the operations we’ll need support for:
- bgen reader (https://github.com/pystatgen/sgkit-bgen/pull/1)
- plink reader (https://github.com/pystatgen/sgkit-plink/pull/1, https://github.com/pystatgen/sgkit-plink/issues/6)
- Variant allele frequency/count (https://github.com/pystatgen/sgkit/issues/29)
- Variant call rate/count (https://github.com/pystatgen/sgkit/issues/29)
- Variant HWE test (https://github.com/pystatgen/sgkit/issues/28)
- Sample call rate/count (https://github.com/pystatgen/sgkit/issues/29)
- An
is_autosomefunction to filter variants by - A function to convert genotype probabilities to hard calls (https://github.com/pystatgen/sgkit/issues/346)
- A linear regression function (https://github.com/pystatgen/sgkit/pull/52)
- A variant annotation function like vep. There are plenty of other ways to get this but an internal function would be great.
- A phenotype normalization pipeline. I don’t expect much of this to become part of sgkit, but there might be some generalizable phenotype-specific functions that are worth considering for inclusion.
There may be a few more beyond that, but I think anything remaining should be reasonable with Xarray/Dask alone.
Issue Analytics
- State:
- Created 3 years ago
- Comments:9 (5 by maintainers)
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@eric-czech I just had a nice chat with @zietzm and @ntatonetti who are at Columbia and are experts in handling complex phenotypes and running many GWAS against them.
They’re interested in using
sgkitand possibly contributing back, particularly on the phenotype side.Would you be open to making https://github.com/related-sciences/ukb-gwas-pipeline-nealelab public soon and potentially working with @zietzm to factor the phenotype handling code into its own repo, maybe something like
sgkit-phenoorphenokit?I’ve been thinking about this one too. I think we’re going to feel Dask’s poor handling of nested data when working with phenotypes, and I’d prefer to keep Spark out of this project as a dependency, so I think we put that code into a separate repo if we find we do need Spark.