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,
David

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator admin
    edited February 2017

    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.

    REVISED
    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 admin

    @davidwb
    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.

    -Sheila

  • shleeshlee CambridgeMember, Broadie, Moderator admin

    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.

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