Build Mutational-Spectrum Catalogs from Variant Call Format Files R package mSigSpectra version 0.1.3 Reads variant call format (VCF) files in a caller-agnostic way, annotates variants with flanking sequence context and transcriptional strand, and builds mutational-spectrum catalogs of single base substitutions (SBS), doublet base substitutions (DBS), and small insertions and deletions (indels, ID) at several resolutions (SBS96, SBS192, SBS1536, DBS78, DBS136, DBS144, ID83, ID89, ID166, ID476) and in both counts and density representations. Successor to the numerical core of the 'ICAMS' package with plotting, 'shiny', and portable document format (PDF) reporting removed; plotting is provided separately by 'mSigPlot'. Used in the preparation of Rozen et al. (2026) <doi:10.5281/zenodo.18451842>. Software Depends: R (>= 4.1) Imports: BSgenome, data.table, fastrc, GenomeInfoDb, GenomicRanges, IRanges, Rcpp, S4Vectors, stats, stringi, tools LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, knitr, mSigPlot, rmarkdown, testthat (>= 3.0.0), withr Steve Rozen <steverozen@pm.me> Comprehensive R Archive Network (CRAN) Steve Rozen [aut, cre], Nanhai Jiang [aut], Arnoud Boot [aut], Mo Liu [aut], Yang Wu [aut], Mi Ni Huang [aut], Jia Geng Chang [aut] GPL-3 2026-09-27 application/tgz https://CRAN.R-project.org/package=mSigSpectra doi:10.32614/CRAN.package.mSigSpectra en-US