What R packages and functions can perform variant calling on .sam and .bam files?

Question

[elvissober]

What R packages and their functions can perform variant calling on .sam and .bam files? Need a commented clear code example. Found RSamtools. No concrete examples in their documentation therein.

Answer 1

[andrew.j.skelton73]

I'm pretty sure you went under the other account name "vassialk"... Any reason why you're mass posting to this site without clarification? Are you a bot? - In reference to your question, I don't think RSamtools implements the variant calling aspects of the package in R. You're better off using a bash based approach to doing variant calling. There are no R packages for running a full variant calling analysis as far as I'm aware.

Answer 2

[Michael]

There is VariantTools in Bioconductor, and here are some introductory slides. (Haven't used it so far.) There are more useful packages in BioC View GenomicVariation.