Load Genotype Data

This is the section where you load the genotype, sample and annotation info into matrices.
This is where everything starts as you provide the data necessary for performing genome wide scans or any other operation that GWASpi permits.

First of all, you need to locate yourself on the desired Study on the GWASpi explorer (1). This is the Study you will organise and store your newly loaded Matrix under. Studies are organizational folders, that help you keep track of your data and any Matrix that will be created by GWASpi will always be located under one. Just the same, the resulting databases, charts and reports will also be stored under subfolders pertaining to a given Study.

Use the “New Matrix Name” and “Description” area (2) to state your future Matrix’s name. Add some information to help you remember what info you are loading. You have up to 2000 characters space. Once the Matrix has finished loading, GWASpi will automatically add the format, the file path of your genotypes, the amount of samples and markers loaded as well as the genotype encoding the data is in.

The “Input” fields (3) is where you will be requested to specify the files that contain your information.

After selecting the format your data is in, the three fields below will ask for the necessary input files you require to complete the loading. Some of these files are compulsory, others will be optional and may be left out.
In case you choose to leave out an optional input file, GWASpi will generate place-holder info. This will allow you to load the data but depending on the data format, will only allow you to perform a limited set of operations. You may, at a later stage, decide to update the missing info and more operations will be available to you from that moment on.

You may learn what input formats are currently accepted in GWASpi here