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mecfs_bio.assets.reference_data.gnomad.gnomad_releases

gnomAD genome sites-VCF releases used for allele-frequency panels.

Files are in the public bucket gnomad-public-us-east-1 (anonymous access, no egress charge to us). Groups and header facts were measured on chr21; see experiments/claude/design_specs/2026-10-02-gnomad-allele-frequency-panel-design.md.

Attributes:

GNOMAD_V2_1_1_GENOMES module-attribute 

GNOMAD_V2_1_1_GENOMES = GnomadRelease(
    name="v2_1_1_genomes",
    build="19",
    vcf_url_template="https://gnomad-public-us-east-1.s3.amazonaws.com/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.{chrom}.vcf.bgz",
    contig_prefix="",
    chromosomes=(*_AUTOSOMES, _X),
    main_groups=("afr", "amr", "asj", "eas", "fin", "nfe"),
    extra_groups=(
        "oth",
        "nfe_nwe",
        "nfe_seu",
        "nfe_onf",
        "nfe_est",
    ),
    header_assembly="gnomAD_GRCh37",
)

GNOMAD_V4_1_GENOMES module-attribute 

GNOMAD_V4_1_GENOMES = GnomadRelease(
    name="v4_1_genomes",
    build="38",
    vcf_url_template="https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr{chrom}.vcf.bgz",
    contig_prefix="chr",
    chromosomes=(*_AUTOSOMES, _X, _Y),
    main_groups=(
        "afr",
        "amr",
        "asj",
        "eas",
        "fin",
        "nfe",
        "sas",
    ),
    extra_groups=("ami", "mid", "remaining"),
    header_assembly="gnomAD_GRCh38",
)