3 Streamline

Zanardi has a specific order in which analyses are run, which cannot be modified (unless you are able to code in python, but doing it at your own risk!). The general scheme is:

In short:

• Red boxes indicate Zanardi's possible input files (single or multiple PLINK or 705 files – see Chapter 3.B for further info)
• Black boxes indicate Zanardi's way to convert the data: 705 files are first transformed to PLINK and then merged if required, multiple files are merged into a single PLINK file over which all analyses are run
• Blue boxes indicate options (analyses available – note this graph gets outdated fast!).
• Straight arrows indicate an (intermediate) step, which is performed by default if the corresponding input file(s) is/are provided. For example: if a single Interbull 705 file is provided, it is converted to PLINK format (PED). If multiple Interbull 705 files are provided (or more than one SNP array is contained in a single 705 file), Zanardi produces first multiple PEDs (as many as SNP arrays are present), and then the files are merged (using PLINK) to create a single PLINK FILE.
• Dashed arrows are the analyses streamlined by Zanardi, thus optional and user defined. A user can choose to run just one, a few or all of them. See Chapter 3.D for further information.
• Asterisk means the option is standalone. Since the dataset is heavily modified, the output of this analysis will terminate the program.