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Add CADD score to variant annotation using dbNSFP

Hi there,

I want to add CADD for the variant annotation, and easily directed to dbNSFP. According to its official site (https://sites.google.com/site/jpopgen/dbNSFP), dbNSFP has integrated CADD.

But when I run snpSift using dbNSFP, CADD is not in the output (while others like SIFT, Polyphen have no problem to be output).

Any suggestion?

Thanks in advance!

snp
• 5,171 views • link
updated by Ram Ram • written by mavershang mavershang

1 answer

You'll need to:

  1. Ensure that the version of dbNSFP that you are using includes CADD
  2. Use the -f argument to SnpSift to tell SnpSift to include CADD in the annotation.

See here: http://snpeff.sourceforge.net/SnpSift.html#dbNSFP

• 1 views • link
updated by Ram Ram • written by Sean Davis Sean Davis

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