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