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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. Log in to SCNbase.org, go to content at the top left, then add content, then downloadable file.
  4. Be ready to add the required info (Title, Organism, very basic pipeline/methods/program versions, and the source of the data).  Make sure to click, "Expose as Jbrowse track".

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

Screenshot of vcf file output