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

Introduction

maftools is a comprehensive toolkit for processing somatic variants from cohort-based cancer genomic studies. maftools offers over 80 functions to perform the most commonly required tasks in cancer genomics, using MAF as the only input file type.

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.

Primary applications

maftools is extremely easy to use, starting with importing an MAF file along with the associated clinical data. Once the data is successfully imported, the resulting MAF object can be passed to various functions. Key applications include:

• Cohort summarization using oncoplots
• Identify co-occurring and mutually exclusive events
• Clinical enrichment analysis
• Detect cancer driver genes
• Infer tumor heterogeneity
• Analyze known cancer signaling pathways
• De-novo somatic signature analysis with NMF
• Compare two cohorts to identify differentially mutated genes
• Perform survival analysis and predict genesets associated with survival
• Drug-gene interactions

Besides the MAF files, maftools can handle sequencing alignment BAM files, copy number output from GISTIC and mosdepth. Please refer to the package documentation sections below to learn more.

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

Moreover, analyzing all 33 TCGA cohorts along with the harmonized clinical data is a breeze.

• A single command tcgaLoad will import the desired TCGA cohort thereby avoiding costly time spent on data mining from public databases.
• Please refer to an associated software package TCGAmutations that provides ready to use MAF objects for 33 TCGA cohorts and 2427 cell line profiles from CCLE - along with relevant clinical information for all sequenced samples.

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

File Fomats	Data portals	Annotation tools
Mutation Annotation Format	TCGA	vcf2maf - for converting your VCF files to MAF
Variant Call Format	ICGC	annovar2maf - for converting annovar output files to MAF
ICGC Simple Somatic Mutation Format	Broad Firehose	bcftools csq - Rapid annotations of VCF files with variant consequences
	cBioPortal	Annovar
	PeCan	Funcotator
	CIViC - Clinical interpretation of variants in cancer
	DGIdb - Information on drug-gene interactions and the druggable genome

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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