Alternate sequence extractor tool/feature?

[esebesty]

I was wondering if a tool exists or would be easy to implement for extracting the alternate sequence based on a variant description and the reference sequence. I'm looking for something that I can include in an R-based pipeline either using a web service, or some c++ code, but had no luck until now (would not want to use GATK, bcf-tools, etc).

The Description extractor is almost what I would need, and I guess the extractor-core code could be used thru Rcpp or I could use the SOAP web-service.

However, instead of a service/function that returns 2C>G for ACGT + AGGT, I'd like something that returns AGGT for 2C>G + ACGT.

Any suggestions on where to look?

[jfjlaros]

Perhaps the mutator library is what you are looking for?

If it is, you might also want to have a look at the reticulate HOWTO.

[esebesty]

Thanks, the mutator library looks like a good start, although it doesn't seem to support all mutation types yet.

[jfjlaros]

Which types are you missing specifically?

[mihailefter]

@esebesty you can now also make use of the mutator from Mutalyzer3, which is also available on PYPI. Make sure that you enable and populate the cache for faster processing times.