Add functionality to get variant triplet context from a list of variant positions and the ref sequence

Question

Add functionality to get variant triplet context from a list of variant positions and the ref sequence

kgori opened this issue 7 years ago · 2 comments

Answer 1 · 2018-12-18T13:56:42.000Z

Maybe the easiest would be to use a C++ library for this? But I guess it would need to be compiled during install. I haven't seen any packages for doing this fast enough outside Bioconductor, but maybe there's a package for fast string processing that we can adapt.

Answer 2 · 2020-03-24T17:03:27.000Z

NB. Rsamtools::scanFa can be used to retrieve regions from a FASTA file.
https://rdrr.io/bioc/Rsamtools/man/scanFa.html