Maftools: Efficient analysis, visualization and summarization of MAF files from large-scale cohort based cancer studies

Mutation Annotation Format (MAF) has become a standard file format for storing somatic/germline variants derived from sequencing of large cohort of cancer samples. MAF files contain a list of all variants detected in a sample along with various annotations associated with the putative variant. MAF file forms the basis for many downstream analyses and provides complete landscape of the cohort. Here we introduce maftools–an R package that provides rich source of functions for performing various analyses, visualizations and summarization of MAF files. Maftools uses data.table library for faster processing/summarization and ggplot2 for generating rich and publication quality visualizations. Maftools also takes advantages of S4 class system for better data representation, with easy to use and flexible functions. Availability and Implementation maftools is implemented as an R package available at https://github.com/PoisonAlien/maftools Contact [email protected]