def get_alt_genotype(ref, alt1, alt2=None):
    """For a given reference allele, and two alternates, return the appropriate
    ALT and GT (genotype) fields for to be written to the VCF

    Args:
        ref (str): reference allele
        alt1 (str): first alternate allele
        alt2 (str): second alternate allele

    Return:
        tuple (vcf_alt, vcf_gt)
        vcf_alt (str):
        vcf_gt (str):
    """
    if alt2 == None:
        alt2 = alt1
    if alt1.upper() == ref.upper() and alt2.upper() == ref.upper():
        vcf_alt = '.'
        vcf_gt = '0/0'
    elif alt1.upper() == alt2.upper():
        vcf_alt = alt1
        vcf_gt = '1/1'
    elif alt1.upper() == ref.upper():
        vcf_alt = alt2
        vcf_gt = '0/1'
    elif alt2.upper() == ref.upper():
        vcf_alt = alt1
        vcf_gt = '0/1'
    else:
        vcf_alt = ','.join([alt1, alt2])
        vcf_gt = '1/2'
    return(vcf_alt, vcf_gt)