Add CADD score to variant annotation using dbNSFP

Question

[mavershang]

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!

[Pierre Lindenbaum]

Hello mavershang!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=58499

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Sean Davis]

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