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Bioconductor / Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
https://bioconductor.org/packages/Rsamtools
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readme

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).