Filter of MuTect2 calls, a separate step in GATK4.

def _mutect2_filter(broad_runner, in_file, out_file, ref_file):
    """Filter of MuTect2 calls, a separate step in GATK4.
    """
    params = ["-T", "FilterMutectCalls", "--reference", ref_file, "--variant", in_file, "--output", out_file]
    return broad_runner.cl_gatk(params, os.path.dirname(out_file))