r-bioc-rsamtools

GNU R binary alignment (BAM), variant call (BCF), or tabix file import
  https://bioconductor.org/packages/Rsamtools/
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This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.