--silent |
To reduce the amount of information printed to stdout.(By default, ATLAS writes out verbose information to stdout.) |
--fixedSeed |
To set seed. Default = Done with random number generator. |
> out.txt |
To redirect the progress report to a file (e.g. out.txt) and save it. Progress is not printed to stdout. |
--logFile logfile_name.txt |
to write the progress report to a log file. Progress is printed to stdout as well. Can be used with --silent to suppress the amount of information printed to stdout. Or append &> logfile_name.txt to the command to write the progress report to a log file to avoid the log from being printed to stdout. |
--out User_defined_name |
To write output files with tag/prefix ‘User_defined_name’ followed by the program generated suffix and file format. |
--refDiv value |
To set the reference divergence to desired value. Default reference divergence = 0.01. |
--baseFreq value_for_A,value_for_C,value_for_G,value_for_T |
To provide user defined base frequencies. Default base frequencies are 0.25 for all four bases. |
--numReadGroups value |
To initialize different numbers of identical read groups. Default is 2. |