1.4 Quickstart

This is a first piece of code you should execute to make sure you have set up ATLAS correctly:

# simulate a BAMfile, aligning to one chromosome of length 1000 with task simulate
/path/to/atlas/build/atlas simulate --chrLength 1000
# run task BAMDiagnostics
/path/to/atlas/build/atlas BAMDiagnostics --bam ATLAS_simulations.bam

As described in the Argument syntax section, ATLAS requires a task name, which can be followed by arguments. Here, the first task name is called simulate and is followed by the argument
--chrLength. This command will simulate an artificial BAMfile with default parameters, except for the chromosome length, which is set to 1000. It will produce the default out-file ATLAS_simulations.bam (see simulate for further information). The second task will assess the sample statistics for the simulated BAMfile (see BAMDiagnostics for further information).

You can get a list of all tasks by typing:

/path/to/atlas/build/atlas