Introduce mutations into sequence using HGVS SVN based nomenclature
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@endre-sebestyen-2707
Last seen 5 weeks ago
Hungary, Budapest

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.

Something like:


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 AGGT.

I know GATK, bcf-tools, etc can do this, but I'd like to use R without external command line tools.

HGVS mutation variant fasta • 75 views
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