Rsamtools is an R/Bioconductor package that provides an interface to the samtools, bcftools, and tabix utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
See https://bioconductor.org/packages/Rsamtools for more information including how to install the release version of the package (please refrain from installing directly from GitHub).