Welcome to HaploTool’s documentation!

HaploTool helps to visualize genomic region of interest (e.g. candidate gene region) and associate haplotype goups to phenotype. It can be used to validate markers by visually and analytically confirming association of a marker with a haplotype that is associated to desirable trait.

Haplotool has the following features:

  • Import data in various formats (HapMap, PLINK)
  • Marker and sample QC and filtering ( see Quality control and filtering )
  • Haplotype clustering into groups and visualization
  • Visualization of phenotype along with genotype ordered according to haplotype groups
  • Testing association between markers and haplotypes

See Quick start page for an example of basic usage.