add release code and resources

[klaricch]

No description provided.

[Copilot]

Pull request overview

This PR adds release code and resources for gnomAD v5, including functions to manage release paths and a comprehensive script to create release sites Hail Tables.

Changes:

• Added new resource functions for release paths and versioned table resources
• Created a complete pipeline script for generating release sites Hail Tables
• Added frequency annotation documentation and version tracking

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 9 comments.

File	Description
gnomad_qc/v5/resources/release.py	Added functions for managing release paths (included datasets JSON, release HT paths) and a versioned table resource, plus frequency README documentation
gnomad_qc/v5/create_release/create_release_sites_ht.py	New script implementing the full release sites HT creation pipeline with configuration management, table joining, and field selection logic

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[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 16 comments.

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[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 9 comments.

Comments suppressed due to low confidence (1)

gnomad_qc/v5/create_release/create_release_utils.py:31

• create_release_sites_ht.py imports remove_missing_vep_fields from this module, but create_release_utils.py doesn't define it, so the release script will fail at import time. Add the missing helper (e.g., port it from gnomad_qc/v4/create_release/create_release_utils.py) or remove the import/usage.

"""Common utils for creating gnomAD v5 genome release."""

import hail as hl

from gnomad_qc.v5.resources.constants import DEFAULT_VEP_VERSION

# Tool versions used in the release that were not on the source tables.
DBSNP_VERSION = "b156"
SIFT_VERSION = "5.2.2"
POLYPHEN_VERSION = "2.2.2"
VRS_SCHEMA_VERSION = "2.0.1"
VRS_PYTHON_VERSION = "2.2.0"
SEQREPO_VERSION = "2024-12-20"

# GENCODE versions by VEP version.
GENCODE_VERSIONS = {
    "105": "Release 39",
    "115": "Release 49",
}
# MANE Select versions by VEP version.
MANE_SELECT_VERSIONS = {
    "105": "v0.95",
    "115": "v1.4",
}
# Backward compatibility: default to DEFAULT_VEP_VERSION.
GENCODE_VERSION = GENCODE_VERSIONS[DEFAULT_VEP_VERSION]
MANE_SELECT_VERSION = MANE_SELECT_VERSIONS[DEFAULT_VEP_VERSION]

# NOTE: VEP 115 annotations were added in v4.1.1.
VEP_VERSIONS_TO_ADD = {"5.0": ["115"]}

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