def get_nonref_alleles(GT_string):
    """Take a VCF genotype (GT) string and return a set containing all non-reference alleles"""
    alleles = set(GT_string.split('/'))
    try:
        alleles.remove('.') # remove missing genotypes
    except KeyError:
        pass
    try:
        alleles.remove('0') # remove reference alleles
    except KeyError:
        pass
    return(alleles)