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

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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.

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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