Run a variant comparison using the bcbio.variation toolkit, given an input configuration.

def bcbio_variation_comparison(config_file, base_dir, data):
    """Run a variant comparison using the bcbio.variation toolkit, given an input configuration.
    """
    tmp_dir = utils.safe_makedir(os.path.join(base_dir, "tmp"))
    resources = config_utils.get_resources("bcbio_variation", data["config"])
    jvm_opts = resources.get("jvm_opts", ["-Xms750m", "-Xmx2g"])
    cmd = ["bcbio-variation"] + jvm_opts + broad.get_default_jvm_opts(tmp_dir) + \
          ["variant-compare", config_file]
    do.run(cmd, "Comparing variant calls using bcbio.variation", data)