Pathr

Pathr is a software tool designed for the analysis and visualization of genomic data, particularly focused on next-generation sequencing (NGS) data. It is developed by the Broad Institute and is part of the GATK (Genome Analysis Toolkit) suite of tools. Pathr is used to identify and visualize genomic regions that are significantly associated with a phenotype or trait of interest. It is particularly useful in the context of exome sequencing and whole-genome sequencing studies, where the goal is to identify genetic variants that are associated with a particular disease or trait.

Pathr operates by taking as input a list of genomic variants and their associated p-values, which are typically obtained from a genome-wide association study (GWAS) or a similar analysis. It then uses a statistical method called the "pathway enrichment analysis" to identify pathways or regions of the genome that are significantly enriched for variants associated with the phenotype of interest. This is done by comparing the distribution of variants in the pathways or regions of interest to the distribution of variants in the rest of the genome.

The output of Pathr is a visualization of the pathways or regions of the genome that are significantly enriched for variants associated with the phenotype of interest. This visualization can be used to identify potential biological mechanisms underlying the phenotype of interest and to generate hypotheses for further experimental validation.

Pathr is a powerful tool for the analysis and visualization of genomic data, and it is widely used in the field of genomics. However, like any software tool, it has its limitations and should be used with caution. It is important to carefully consider the assumptions and limitations of the statistical methods used by Pathr, and to interpret the results in the context of the specific biological question being addressed.