How do I upload a vcf file?

Tabix is a program that is necessary to be able to index the vcf file for upload and display in Jbrowse.  Once this program is installed, the process is fairly easy.

Be aware that your scaffold names must match the Jbrowse scaffold names in every respect (capitalization, underscores, numbering, etc). Also, the vcf does not necessarily need to be sorted, which is different from all other file types.

  1. Zip your file with bgzip.  As simple as "bgzip file.vcf"
  2. Index your zipped file with tabix.  "tabix -p vcf  file.vcf.gz"
  3. Go to, click JBrowse, select your specific genome, then click tracks.
  4. You will then have to upload your compressed vcf file and your vcf index by clicking "Select Files", adding your respective files, and then clicking "Open".                                                           

Your vcf file output will look similar to the "SNPs across 15 populations of H. glycines" track below from the TN10 Draft.

Screenshot of vcf file output