finding functional rare and synonymous alleles in a vcf file
Hello,
I have to identify both rare synonymous and and functional variants in a humans exome for each gene region.
I know there are some ready to use tools , bus also was suggested not to trust them very much.
Is it true?
I think I will need to start to write my own script, but have no idea, with what to start my code.
So, any suggestions will be appreciated.
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storm1907 •
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Who said that, and why do you trust them? What exactly did you hear?
Some other bioinformaticians; but maybe it is not true. I also think that for such simple purpose there must be ready solutions. Anyway, I will be happy about some advice, which tool to use; Also, it could be interesting to write home made code for learning purposes
You could try VEP or ANNOVAR and look for synonymous variants that fall in exonic splice regions, for example - those are both synonymous and "functional".