Kl/info ht #732
Kl/info ht #732
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Pull request overview
This PR adds resources and a script for generating variant QC annotations for gnomAD v5. The key changes include correcting the annotations root path, adding new annotation resources (info HTable and VCF paths), and implementing a script to import and reformat VCF annotations.
- Corrected the annotations root path from "sample_qc" to "annotations"
- Added
get_info_ht()function and VCF-related constants for variant QC annotations - Created a new script to generate variant QC annotations from AoU annotated VCF files
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
| gnomad_qc/v5/resources/annotations.py | Corrected path suffix, added import for get_checkpoint_path, and added variant QC annotation resources including get_info_ht() function and VCF constants |
| gnomad_qc/v5/annotations/generate_variant_qc_annotations.py | New script implementing VCF import, annotation reformatting, and AS_lowqual calculation for variant QC |
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Co-authored-by: Copilot <[email protected]>
mike-w-wilson
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mike-w-wilson
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This looks good overall. I think we should just build in the option to run on batch though in hopeful anticipation...
| def main(args): | ||
| """Generate all variant annotations needed for variant QC.""" | ||
| hl.init( | ||
| log="/home/jupyter/workspaces/gnomadproduction/variant_qc_annotations.log", |
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If we run this in batch, which is the goal, we should change this log path
| finally: | ||
| logger.info("Copying hail log to logging bucket...") | ||
| hl.copy_log( | ||
| get_logging_path("generate_variant_qc_annotations", environment="rwb") |
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Lets build in the option for a passed env, e..g batch.
Co-authored-by: Mike Wilson <[email protected]>
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