Quick start

You need a genomic variant dataset in either HapMap ( GOBii HapMap supported) or binary PLINK format.

The HaploTool R package distribution comes with a few example rice datasets stored in the folder “extdata”

A typical workflow could start like this:

Importing data

  • In the Import tab, browse to a genotype input file and select it.

In case of multiple files (e.g. a PLINK binary dataset - .bed, .bim, and .fam files), select all files that constitute one dataset.

  • Select the file type in the dropdown and click Import button

If the file has been imported, you will see a new dataset name appear in the “Datasets” dropdown list in the navigation bar (navbar) on the left.

Similarly, you can input a phenotype file. Having a phenotype is not required, except for the last step - marker validation.

Note. Haplotool is intended to be used with genotype data from a relatively short genomic region (so that number of distinct haplotypes is small). If you upload a genome-wide or chromosome-wide data, you will need to select a region in the Filtering tab, to have meaningful results.

Filtering and quality control

This step is optional, althogh useful to perform on new datasets.

Clicking on the Filter menu in the navbar, one can perform various forms of filtering and quality control. ( for details please go to Quality control and filtering).

You can skip this step on your first run of HaploTool.

Visualizing haplotype groups

Select the Analysis menu item in the navigation bar on the left.

Select any estimate of the number of haplotypes you expect to see in this genomic region and click “Generate plot”.

You can also upload phenotype in the “Input” tab and check “Include phenotype” in the “Analysis” tab to have the phenotype visualized along with genotype.

Marker validation

See the full documentation for this usage.