mecfs_bio.assets.reference_data.genomic_sem_reference.hapmap3_snpist

Genomic SEM requires a reference file containing a list of SNPs to use for ldsc. Usually, these consist of the hapmap3 SNPs

The Task here downloads the reference file recommended by the GenomicSEM tutorial. See" https://github.com/GenomicSEM/GenomicSEM/wiki/3.-Genome%E2%80%90wide-Models

I have rehosted the file on dropbox.

Attributes:

• HAPMAP3_SNPLIST_FOR_GENOMIC_SEM –

HAPMAP3_SNPLIST_FOR_GENOMIC_SEM module-attribute

HAPMAP3_SNPLIST_FOR_GENOMIC_SEM = DownloadFileTask(
    meta=ReferenceFileMeta(
        group="genomic_sem_reference",
        sub_group="hapmap",
        sub_folder=PurePath("raw"),
        id=AssetId("hapmap3_snp_list"),
        extension=".snplist",
        filename="w_hm3",
    ),
    url="https://www.dropbox.com/scl/fi/8dsoz94erkkv3fdln1mhb/w_hm3.snplist?rlkey=59lhbaz7bvj3bv669f87fsufg&dl=1",
    md5_hash="e1372a59749eb1f92f7f6931c075f5ac",
)