Alternate sequence extractor tool/feature?
Created by: 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?