text: user35: Are there any good options for calling variants or even just a pileup from R? R is not ideal for this, but I'd like to integrate with other functions.
  I found deepSNV::bam2R which roughly does what I am looking for. Are there any alternatives?
  
  user2108: Samtools/bcftools/tabix is available in R via Rsamtools.
  SEQprocess also provides wrappers for different tools such as GATK and bowtie.
  More utility packages are noted here.
  
original_text: 35: <p>Are there any good options for calling variants or even just a pileup from R? R is not ideal for this, but I'd like to integrate with other functions.</p>
  <p>I found <a href="https://www.rdocumentation.org/packages/deepSNV/versions/1.18.3/topics/bam2R" rel="nofollow noreferrer">deepSNV::bam2R</a> which roughly does what I am looking for. Are there any alternatives?</p>
   2108: <p>Samtools/bcftools/tabix is available in R via <a href="https://kasperdanielhansen.github.io/genbioconductor/html/Rsamtools.html" rel="nofollow noreferrer">Rsamtools</a>.</p>
  <p><a href="https://github.com/omicsCore/SEQprocess/blob/master/Reference_Manual.pdf" rel="nofollow noreferrer">SEQprocess</a> also provides wrappers for different tools such as GATK and bowtie.</p>
  <p>More utility packages are noted <a href="https://docs.rc.fas.harvard.edu/kb/ngs-analysis-with-r/" rel="nofollow noreferrer">here</a>.</p>
  