How to use the gnomad.resources.grch37.reference_data function in gnomad

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github macarthur-lab / gnomad_hail / gnomad / utils / filtering.py View on Github external
criteria = []
    if filter_lcr:
        lcr = resources.lcr_intervals.ht()
        criteria.append(hl.is_missing(lcr[mt.locus]))

    if filter_decoy:
        decoy = resources.decoy_intervals.ht()
        criteria.append(hl.is_missing(decoy[mt.locus]))

    if filter_segdup:
        segdup = resources.seg_dup_intervals.ht()
        criteria.append(hl.is_missing(segdup[mt.locus]))

    if filter_exome_low_coverage_regions:
        high_cov = resources.high_coverage_intervals.ht()
        criteria.append(hl.is_missing(high_cov[mt.locus]))

    if high_conf_regions is not None:
        for region in high_conf_regions:
            region = hl.import_locus_intervals(region)
            criteria.append(hl.is_defined(region[mt.locus]))

    if criteria:
        filter_criteria = functools.reduce(operator.iand, criteria)
        if isinstance(mt, hl.MatrixTable):
            mt = mt.filter_rows(filter_criteria)
        else:
            mt = mt.filter(filter_criteria)

    return mt
github macarthur-lab / gnomad_hail / gnomad / utils / filtering.py View on Github external
:param filter_lcr: Whether to filter LCR regions
    :param filter_decoy: Whether to filter decoy regions
    :param filter_segdup: Whether to filter Segdup regions
    :param filter_exome_low_coverage_regions: Whether to filter exome low confidence regions
    :param high_conf_regions: Paths to set of high confidence regions to restrict to (union of regions)
    :return: MatrixTable or Table with low confidence regions removed
    """
    build = get_reference_genome(mt.locus).name
    if build == "GRCh37":
        import gnomad.resources.grch37.reference_data as resources
    elif build == "GRCh38":
        import gnomad.resources.grch38.reference_data as resources

    criteria = []
    if filter_lcr:
        lcr = resources.lcr_intervals.ht()
        criteria.append(hl.is_missing(lcr[mt.locus]))

    if filter_decoy:
        decoy = resources.decoy_intervals.ht()
        criteria.append(hl.is_missing(decoy[mt.locus]))

    if filter_segdup:
        segdup = resources.seg_dup_intervals.ht()
        criteria.append(hl.is_missing(segdup[mt.locus]))

    if filter_exome_low_coverage_regions:
        high_cov = resources.high_coverage_intervals.ht()
        criteria.append(hl.is_missing(high_cov[mt.locus]))

    if high_conf_regions is not None:
        for region in high_conf_regions: