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Pull request overview
Adds support for exporting the v5 variant-QC “info” Hail Table as a sites-only VCF, including a new resource helper for the expected VCF output path.
Changes:
- Add
info_vcf_path(...)resource helper to provide the output path for the exported info VCF. - Add a
--export-info-vcfflag to generate and export the info HT as a VCF (with Tabix index), usingadjust_vcf_incompatible_types.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
gnomad_qc/v5/resources/annotations.py |
Adds a helper to standardize the output path for the exported info VCF. |
gnomad_qc/v5/annotations/generate_variant_qc_annotations.py |
Adds a CLI flag and implementation to export the info HT to a VCF. |
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