Question: What R packages and functions can perform variant calling on .sam and .bam files?
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gravatar for elvissober
4.9 years ago by
elvissober20
South Africa
elvissober20 wrote:

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.

R sequence wgs sequencing • 2.6k views
ADD COMMENTlink modified 4.9 years ago by Michael Dondrup48k • written 4.9 years ago by elvissober20
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gravatar for andrew.j.skelton73
4.9 years ago by
London
andrew.j.skelton736.0k wrote:

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.

ADD COMMENTlink modified 11 months ago by _r_am30k • written 4.9 years ago by andrew.j.skelton736.0k
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gravatar for Michael Dondrup
4.9 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

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.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Michael Dondrup48k
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