Is there a Bioconductor package that is able to convert a reference sequence + HGVS SVN specification into an edited sequence? Couldn't find one, but I might be just looking at the wrong packages.
edited_sequence <- get_variant_seq("ENST00000357654.9:c.1045G>T")
and it returns a fasta string with the ENST00000357654.9 transcript sequence edited at position 1045.
Or something like this:
seq1 <- "ACGT" mut1 <- "c.2C>G" edited_sequence <- get_variant_seq(sequence = seq1, mutation = mut1)
and it return
I know GATK, bcf-tools, etc can do this, but I'd like to use R without external command line tools.