The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

How can I annotate with dbsnp and also include info fields from dbsnp vcf?

davidwbdavidwb Park City, UTMember

I want to annotate my vcf using dbsnp, however I don't want to add only the dbsnp rs#s in the ID field. I also want to add INFO fields from the dbsnp vcf into the annotated vcf. How can this be achieved?

I tried to do it by running the command below, but this did not work.

java -jar GenomeAnalysisTK.jar \
   -R ucsc.hg19.fasta \
   -T VariantAnnotator \
   -V gatk.vcf \
   -o gatk_dbsnp138.vcf \
   --dbsnp dbsnp_138.hg19.vcf \
   --resource:dbsnp dbsnp_138.hg19.vcf \
   --expression dbsnp.CLNSIG \
   --expression dbsnp.CLNACC   

Thanks very much,


  • shleeshlee CambridgeMember, Broadie, Moderator
    edited February 17

    Hi @davidwb,

    I'm entering some murky territory here in terms of my knowledge but the rest of the team is away so let me tentatively suggest a few things that I hope moves you in the right direction.

    What happens when you run the command? Did it not give the correct results or did it fail with an error?

    Post edited by shlee on
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    Hi David,

    Which version are you using? I just tried with version 3.7, and I get some dbsnp annotations added to my input VCF. I ran pretty much the exact same command you ran.


  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @davidwb. I'm revisiting your question because I recently just did what you are asking for--annotate INFO field columns from dbSNP. If you are still interested, I can share with you my steps.

Sign In or Register to comment.