Introduce mutations into sequence using HGVS SVN based nomenclature
Entering edit mode
Last seen 10 months 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 • 286 views

Login before adding your answer.

Traffic: 513 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6