# GARCOM: A user-friendly R package for genetic mutation counts

## TL;DR

GARCOM is an R package that simplifies counting genetic mutations within specific regions using NGS data.

## Contribution

GARCOM introduces a user-friendly tool for efficiently calculating allelic counts within genetic boundaries.

## Key findings

- GARCOM processes PLINK or VCF formatted data to generate mutation count matrices.
- The package supports data subsetting for refined genetic analyses.
- It provides a straightforward solution for a task previously requiring complex coding.

## Abstract

Next-generation sequencing (NGS) has enabled analysis of rare and uncommon variants in large study cohorts. A common strategy to overcome these low frequencies and/or small effect sizes relies on collapsing strategies, i.e. to bin variants within genes/regions. Several tools are now available for advanced statistical analyses however, tools to perform basic tasks such as obtaining allelic counts within defined genetics boundaries are unavailable or require complex coding. GARCOM library, an open-source freely available package in R language, returns a matrix with allelic counts within defined genetic boundaries. GARCOM accepts input data in PLINK or VCF formats, with additional options to subset data for refined analyses.