def getAlleles(ref, alt, gt):
    """
    Given ref alt and gt, return a list of alleles at site

    :param ref: str
        Reference allele

    :param alt: list
        List of alt alleles at site

    :param gt: list
        Genotype at site

    :return: set
        Set of alleles at site
    """
    if gt is None:
        return None;
    allAlleles = [ref] + alt;
    return set([allAlleles[i] for i in gt]);