I'm still a beginner and using [Illumina Platinum Genomes as a toy dataset][1]. Google supplies the files in VCF, but I need them annotated with rsIDs.

I've tried GATK VariantAnnotator and bcftools annotate [as suggested by this post I found via Google][2] and [this Biostars post][3], but I'm not having any luck.

When the command line finishes running, the output doesn't have the rsIDs filled in and no obvious errors pop up. I'm kinda stumped.

Any help is appreciated.


  [1]: https://cloud.google.com/genomics/docs/public-datasets/illumina-platinum-genomes
  [2]: https://gist.github.com/obenshaindw/99440ac43de07548e453
  [3]: https://www.biostars.org/p/160021/
Hey it's quite some time ago but if anyone else is having a problem I just wanted to say following command worked for me:

    bcftools annotate -a /data/references/hg19/pipe/dbsnp138/00-All.vcf.gz -c ID -o samtools_annotated.vcf.gz samtools.vcf.gz

The thing to look out for is, I think it doesn't work if your reference has numeric chromosome column while your VCF file has it as with 'chr' added to is, *e.g.* "chr1". 