README.md
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

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.

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

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

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

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

| 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 | |

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)