Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-03-01T19:25:29.497Z
Answers.LastActivityDate: 2021-03-01T19:25:29.497Z
Answers.UserDisplayName: Maximilian Press
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-11T12:18:30.203Z
Comments.Text: You can always call out to the shell from R. Do you need the solution to be pure R, or could it be a library hosted on CRAN, bioconductor, or even conda? How are you controlling your dependencies?
Comments.UserDisplayName: winni2k
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-13T02:50:47.577Z
Comments.Text: @winni2k I was just looking for an R package. I am assuming the package is taking care of any dependencies.
Comments.UserDisplayName: burger
Tags: <r><sam><variant-calling><genotyping><variants>
Title: genotyping or variant calling in R
ThreadText: # genotyping or variant calling in R
  
  (Asked by: username_0 on 2021-03-01)
  
  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](https://www.rdocumentation.org/packages/deepSNV/versions/1.18.3/topics/bam2R) which roughly does what I am looking for. Are there any alternatives?
  
  **Tags:** r, sam, variant-calling, genotyping, variants
  
  > **Comments:**
  > **username_1**: You can always call out to the shell from R. Do you need the solution to be pure R, or could it be a library hosted on CRAN, bioconductor, or even conda? How are you controlling your dependencies?  
  > **username_0**: @username_1 I was just looking for an R package. I am assuming the package is taking care of any dependencies.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-03-01. Score: 1
  
  Samtools/bcftools/tabix is available in R via [Rsamtools](https://kasperdanielhansen.github.io/genbioconductor/html/Rsamtools.html).
  
  [SEQprocess](https://github.com/omicsCore/SEQprocess/blob/master/Reference_Manual.pdf) also provides wrappers for different tools such as GATK and bowtie.
  
  More utility packages are noted [here](https://docs.rc.fas.harvard.edu/kb/ngs-analysis-with-r/).
  
  
  ---
  
  