finding functional rare and synonymous alleles in a vcf file

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3.3 years ago

storm1907 ▴ 30

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.

exome variants • 921 views

ADD COMMENT • link updated 3.3 years ago by Ram 44k • written 3.3 years ago by storm1907 ▴ 30

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I know there are some ready to use tools , bus also was suggested not to trust them very much.

Who said that, and why do you trust them? What exactly did you hear?

ADD REPLY • link 3.3 years ago by Ram 44k

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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

ADD REPLY • link 3.3 years ago by storm1907 ▴ 30

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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".

ADD REPLY • link 3.3 years ago by Ram 44k

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