Maftools Save

maftools - An R package to summarize, analyze and visualize MAF files

Introduction

maftools provides a comprehensive set of functions for processing MAF files and to perform most commonly used analyses in cancer genomics. See here for a detailed usage and a case study.

Installation

#Install from Bioconductor repository
BiocManager::install("maftools")

#Install from GitHub repository
BiocManager::install("PoisonAlien/maftools")

Getting started: Vignette and a case study

A complete documentation of maftools using TCGA LAML as a case study can be found here.

Besides the MAF files, maftools also facilitates processing of BAM files. Please refer to below vignettes and sections to learn more.

• Copy number analysis with ASCAT and mosdepth
• Generate personalized cancer report for known somatic hotspots
• Sample mismatch and relatedness analysis

Citation

Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. 2018. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Research. PMID: 30341162

Useful links

Useful packages/tools

Below are some more useful software packages for somatic variant analysis

• TRONCO - Repository of the TRanslational ONCOlogy library (R)
• dndscv - dN/dS methods to quantify selection in cancer and somatic evolution (R)
• cloneevol - Inferring and visualizing clonal evolution in multi-sample cancer sequencing (R)
• sigminer - Primarily for signature analysis and visualization in R. Supports maftools output (R)
• GenVisR - Primarily for visualization (R)
• comut - Primarily for visualization (Python)
• TCGAmutations - pre-compiled curated somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project) that can be loaded into maftools (R)
• somaticfreq - rapid genotyping of known somatic hotspot variants from the tumor BAM files. Generates a browsable/sharable HTML report. (C)

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