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
maftoolsoutput (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)