Hi,
I have mutations with an absolute Position, Chromosome and context e.g.:
Chr Pos Ref Alt Context
chr21 36252877 C T Coding,Intergenic
So i found out with my python script, that it's in this example the gene DOPEY2 and now I am searching for a way to get all possible protein sequences that are affected by this mutation.
Any help is appreciated.
PS: I downloaded the hg19 genome and gathered the DNA Sequences of the genes, but i need the splicing informations for further progress.
Update: I still don't know the exact solution, but for anyone with a similar problem, have a look at ANNOVAR Documentation,Coding_Change
Please use
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to reply to earlier answers, as such this thread remains logically structured and easy to follow.I wasn't aware that Annovar provided more information than VEP, but good that you found what you need.