First draft of Toolbox use cases #4
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this file is needed to create a python package with this repo, right? so we would want to keep it |
I will try to solve the cluster issue when it circles back. |
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- Add a description of the repo structure to the README - Add some potential requirements - Update the documentation and make sure it works - Create a notebook specific to loading gnomAD release data and just showing what each dataset looks like.
- Add a description of the repo structure to the README - Add some potential requirements - Update the documentation and make sure it works - Create a notebook specific to loading gnomAD release data and just showing what each dataset looks like.
- Addition of variant.py to store some functions that can also be used by frequency based filtering - Changes to frequency filtering to use new default settings if not passed a ht
Co-authored-by: Qin He <44242118+KoalaQin@users.noreply.github.com>
Suggestions on the initial toolbox PR
jkgoodrich
approved these changes
Dec 18, 2024
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This PR includes the following examples:
Get variant count
Filter to variants by VEP annotations
Get 'freq' for specific genetic ancestry groups
I also removed the "setup.py" because it caused problems while starting a cluster, we have 'setup.py' in gnomad_methods, but we don't have it in gnomad_qc, do we really need it here?