GATK 4.1.0.0 outputs variants that have missing ALTs, which breaks downstream
    tools, this filters those out.

def gatk_remove_missingalt(in_file, data):
    """
    GATK 4.1.0.0 outputs variants that have missing ALTs, which breaks downstream
    tools, this filters those out.
    """
    base = in_file.split('.vcf.gz')[0]
    out_file = "%s-nomissingalt%s" % (base, '.vcf.gz')
    if utils.file_exists(out_file):
        return out_file
    no_gzip_out = out_file.replace(".vcf.gz", ".vcf")
    with file_transaction(no_gzip_out) as tx_out_file:
        with utils.open_gzipsafe(in_file) as in_handle, open(tx_out_file, "w") as out_handle:
            for line in in_handle:
                line = remove_missingalt(line)
                if line:
                    out_handle.write(line)
    return vcfutils.bgzip_and_index(no_gzip_out, data["config"])