<img src="vignettes/maftools_hex.svg" align="left" height="140" /></a> ## maftools - An R package to summarize, analyze and visualize MAF files [](https://github.com/poisonalien/maftools/issues) [](https://github.com/PoisonAlien/maftools/actions) ## Introduction `maftools` provides a comprehensive set of functions for processing [MAF](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/) files and to perform most commonly used analyses in cancer genomics. See [here](http://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html) for a detailed usage and a case study. ## Installation ```{r} #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](https://www.nejm.org/doi/full/10.1056/nejmoa1301689) as a case study can be found [here](http://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html). <p align="left"> <img src="https://user-images.githubusercontent.com/8164062/97981605-d8a59500-1dd2-11eb-9f5e-cc808f7b3f91.gif" height="320" height="400"> </p> Besides the MAF files, maftools also facilitates processing of BAM files. Please refer to below vignettes and sections to learn more. - [Copy number analysis](https://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/cnv_analysis.html) with [ASCAT](https://github.com/VanLoo-lab/ascat) and [mosdepth](https://github.com/brentp/mosdepth) - [Generate personalized cancer report](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/cancer_hotspots.html) for known somatic [hotspots](https://www.cancerhotspots.org/) - [Sample mismatch and relatedness analysis](https://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html#12_Sample_swap_identification) ## Citation **_Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. 2018. Maftools: efficient and comprehensive analysis of somatic variants in cancer. [Genome Research](https://doi.org/10.1101/gr.239244.118). PMID: [30341162](https://www.ncbi.nlm.nih.gov/pubmed/?term=30341162)_** ## Useful links | File Fomats | Data portals | Annotation tools | |--------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------| | [Mutation Annotation Format](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/) | [TCGA](http://cancergenome.nih.gov) | [vcf2maf](https://github.com/mskcc/vcf2maf) - for converting your VCF files to MAF | | [Variant Call Format](https://en.wikipedia.org/wiki/Variant_Call_Format) | [ICGC](https://docs.icgc.org/) | [annovar2maf](https://github.com/PoisonAlien/annovar2maf) - for converting annovar output files to MAF | | ICGC [Simple Somatic Mutation Format](https://docs.icgc.org/submission/guide/icgc-simple-somatic-mutation-format/) | [Broad Firehose](https://gdac.broadinstitute.org/) | [bcftools csq](https://samtools.github.io/bcftools/howtos/csq-calling.html) - Rapid annotations of VCF files with variant consequences | | | [cBioPortal](https://www.cbioportal.org/) | [Annovar](https://annovar.openbioinformatics.org/en/latest/) | | | [PeCan](https://pecan.stjude.cloud/) | [Funcotator](https://gatk.broadinstitute.org/hc/en-us/articles/360037224432-Funcotator) | | | [CIViC](https://civicdb.org/home) - Clinical interpretation of variants in cancer | | | | [DGIdb](http://www.dgidb.org/) - Information on drug-gene interactions and the druggable genome | | ## Useful packages/tools Below are some more useful software packages for somatic variant analysis * [TRONCO](https://github.com/BIMIB-DISCo/TRONCO) - Repository of the TRanslational ONCOlogy library (R) * [dndscv](https://github.com/im3sanger/dndscv) - dN/dS methods to quantify selection in cancer and somatic evolution (R) * [cloneevol](https://github.com/hdng/clonevol) - Inferring and visualizing clonal evolution in multi-sample cancer sequencing (R) * [sigminer](https://github.com/ShixiangWang/sigminer) - Primarily for signature analysis and visualization in R. Supports `maftools` output (R) * [GenVisR](https://github.com/griffithlab/GenVisR) - Primarily for visualization (R) * [comut](https://github.com/vanallenlab/comut) - Primarily for visualization (Python) * [TCGAmutations](https://github.com/PoisonAlien/TCGAmutations) - pre-compiled curated somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project) that can be loaded into `maftools` (R) * [somaticfreq](<https://github.com/PoisonAlien/somaticfreq>) - rapid genotyping of known somatic hotspot variants from the tumor BAM files. Generates a browsable/sharable HTML report. (C) *** #### Powered By * [data.table](https://github.com/Rdatatable/data.table/wiki) at [warp speed](https://en.wikipedia.org/wiki/Warp_drive)