Issue with dbNSFP using SnpSift

Question

[aidangcruickshank]

Hi everyone,

I'm having trouble annotating a VCF with SnpSift and the dbnsfp option. From the documentation, running:

java -jar SnpSift.jar dbnsfp -v -db path/to/db path/to/vcf > out.vcf 

...should annotate for all fields in the database. However, it seems that my files are only being annotated for a subset of the fields which show up in a list of "fields to add" which are listed in a stdout list. I did a quick grep of the config file for dbnsfp and looked around but didn't find anything. Is there any way to change the fields that are being annotated for? I would like to add all annotations, but understanding what's happening here is my main concern. I'm probably being a tad dense here.

Thanks, Aidan

Answer 1

[Ram]

...should annotate for all fields in the database

Your expectations are not correct. See the documentation:

You can now specify which fields you want to use for annotation using the -f command line option followed by a comma separated list of field names. Defaults fields are shown when running the command without any arguments java -jar SnpSift.jar dbNSFP

[aidangcruickshank]

I found this just as you replied. As I thought, I was being dense.

[Ram]

That happens. More often than not, I've encountered solutions as I was typing a post for submission here.

In any case, I've moved my comment to an answer. Please accept it to provide closure to the post.