My suggestion would be to make this as one big command line so the flow is more clear:

    freebayes = config_utils.get_program("freebayes", config)
    opts = _freebayes_options_from_config(items, config["algorithm"],
                                          out_file, region)
    cl = ("{freebayes} --pooled-discrete --pvar 0.7 --genotype-qualities "
          "{opts} {tumor_bam} {normal_bam}"
          " | {vcfsamplediff} -s VT {normal_name} {tumor_name} - >"
          " {tx_out_file}")