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[datasets] update gnomAD datasets available via Datasets API/Annotation DB - #11608

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danking merged 3 commits into
hail-is:mainfrom
pwc2:update-gnomad-datasets
Mar 24, 2022
Merged

danking merged 3 commits into
hail-is:mainfrom
pwc2:update-gnomad-datasets

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@pwc2

@pwc2 pwc2 commented Mar 17, 2022

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Not all of the Hail Tables and MatrixTables that are publicly available on the gnomAD downloads page are currently available in the Datasets API/Annotation DB.

This PR makes the following changes to the datasets available via the Hail Datasets API/Annotation DB:

  • Add gnomad_genome_sites Table, versions: 3.1.1, 3.1.2
  • Add gnomad_hgdp_1kg_subset_dense MatrixTable, version: 3.1.2
  • Rename gnomad_hgdp_1kg_callset MatrixTable to gnomad_hgdp_1kg_subset_dense, version: 3.1
  • Add gnomad_hgdp_1kg_subset_sparse MatrixTable, version: 3.1.2
  • Add gnomad_hgdp_1kg_subset_sample_metadata Table, version: 3.1.2
  • Add gnomad_hgdp_1kg_subset_variant_annotations Table, version: 3.1.2
  • Add gnomad_variant_co-occurrence Table, version: 2.1.1
  • Add gnomad_pca_variant_loadings Table, versions: 2.1, 3.1

Other general changes:

  • Add/update the schema .rst files, for the datasets listed above, for the docs
  • Set the example dataset loaded in hl.experimental.load_dataset to be the most recent gnomad_hgdp_1kg_subset_dense MatrixTable (version 3.1.2)

@pwc2
pwc2 requested a review from danking March 17, 2022 00:48

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I spot-checked a few of them, they all looked good. One comment about updating to at least the most recent major version for our example schema.

Comment thread hail/python/hail/docs/datasets/schemas/gnomad_genome_sites.rst
@pwc2
pwc2 force-pushed the update-gnomad-datasets branch from e3b1ad4 to 8b2f8dd Compare March 18, 2022 15:05
@pwc2
pwc2 requested a review from danking March 18, 2022 15:14
@pwc2
pwc2 dismissed danking’s stale review March 18, 2022 15:15

updated schemas

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Thank you much, this is a great improvement!

@danking
danking merged commit a1030f6 into hail-is:main Mar 24, 2022
@pwc2
pwc2 deleted the update-gnomad-datasets branch March 29, 2022 15:54
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2 participants