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

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.

sequencing sequence wgs r
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updated by Ram Ram • written by elvissober • elvissober

2 answers

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.

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updated by Ram Ram • written by andrew.j.skelton73 andrew.j.skelton73

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.

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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

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