Question

What is the best annotation tool?

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2.7 years ago

Sonia • 0

Hi all,

I want to annotate ~200 VCF files for cancer patients. my question is that what's the best tool for annotating these bulk files? Do you recommend using multiple tools and merge the results?

Thanks for any help

VCF annotation • 1.5k views

ADD COMMENT • link updated 2.7 years ago by colindaven 6.3k • written 2.7 years ago by Sonia • 0

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What sort of annotations you are looking for??

ADD REPLY • link 2.7 years ago by Nitin Narwade ★ 1.6k

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Dear Nitin, I'm not sure if I correctly understood what you mean, but I want to use the stand-alone tools and need to annotate the somatic mutations by them.

ADD REPLY • link 2.7 years ago by Sonia • 0

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What kind of data do you have?

ADD REPLY • link 2.7 years ago by ponganta ▴ 590

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Dear ponganta,

I have the VCF files of the WGS and want to annotate them.

ADD REPLY • link 2.7 years ago by Sonia • 0

score 2 · Answer 1 · 2021-07-25

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2.7 years ago

Kevin Blighe 87k

Over the years, the ones that I have used most are:

Variant Effect Predictor (VEP)
ANNOVAR

Both require some concentrated setup time, but, once done, they'll be your friends for life.

Kevin

ADD COMMENT • link 2.7 years ago by Kevin Blighe 87k

score 2 · Answer 2 · 2021-07-26

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2.7 years ago

colindaven 6.3k

VEP is very nice.
SNPeff is popular.

More info here:

updated clinical variant annotation software and databases

ADD COMMENT • link 2.7 years ago by colindaven 6.3k