mecfs_bio.assets.reference_data.thousand_genomes.eur_hg19_vcf

The 1000 Genomes phase 3 EUR reference VCF (hg19), self-hosted and pinned by checksum.

This is gwaslab's 1kg_eur_hg19 panel: multi-allelic variants are decomposed, variants are normalized, and INFO/AF carries the EUR allele frequency. Records are indexed for chromosomes 1-22 and X only.

It is rehosted rather than fetched from gwaslab's own URL, for the same reasons as eur_hg38_30x_vcf.py: gwaslab republishes its panels in place, and by September 2026 the gwaslab link for this file served a "File Deleted" page. The copy hosted here was taken from a local gwaslab download whose md5 matched gwaslab's catalogue entry.

The checksum below is what pins the content.

Attributes:

• THOUSAND_GENOMES_EUR_HG19_VCF –

THOUSAND_GENOMES_EUR_HG19_VCF module-attribute

THOUSAND_GENOMES_EUR_HG19_VCF = DownloadFileTask(
    meta=ReferenceFileMeta(
        id="thousand_genomes_eur_hg19_vcf",
        group="thousand_genomes",
        sub_group="eur_hg19",
        sub_folder=PurePath("raw"),
        extension=".vcf.gz",
    ),
    url="https://www.dropbox.com/scl/fi/q3wndz2wockuqto5pq0cc/EUR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz?rlkey=zq8fzrjtbbl20r1wr74p4tqa1&dl=1",
    md5_hash="2c78cb84cb1f90b576510decc45e5b9b",
)