annotate MAF with triplet context

morinlab / GAMBLR

Set of standardized functions to operate with genomic data

https://morinlab.github.io/GAMBLR/

MIT License

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annotate MAF with triplet context #222

Closed rdmorin closed 9 months ago

rdmorin commented 1 year ago

Can we add functionality to GAMBLR to allow users to annotate MAFs with the triplet context (mutated base with adjacent -1 and +1)? Ideally we should also support (optionally) converting to the reverse complement according to the direction of transcription.

e.g. Mutation C>T Hypothetical triplet sequence context extracted from reference genome: GCA If the affected gene is on the opposite strand: TGC

rdmorin commented 9 months ago

@HoumanLM is this complete?

HoumanLM commented 9 months ago

@rdmorin I pushed the new code, I need your confirmation to start modifying its documentation. Then, it will be okay!

HoumanLM commented 9 months ago

Now, I believe this issue has also been posted in the following link: https://github.com/morinlab/GAMBLR.results/issues/24