Walnut SNP data

[mestato]

Contacted by Annarita Marrano and Randi Famula to add SNP data for walnut (J. regia). Currently have vcf file, have sent email to ask:

• should this be embedded with genome version 2.0 or its own separate thing?
• should we go ahead and throw up a JBrowse with this is a track?
• should we add email for Randi and/or Annarita
• any description?

Awaiting reply.

[almasaeed2010]

This could be a good time to train the undergrads to add the track using the new jbrowse module if we end up needing one.

[mestato]

Info from Randi:

Paper is submitted but not yet accepted: Famula, R.A., Richards, J.A., Famula, T.R., & Neale, D.B. (2018). Association genetics of carbon isotope discrimination and leaf morphology in a breeding population of Juglans regia L. Tree Genetics & Genomes. Information regarding the cultivars/accessions IDs can be found in Table S2.

No need for a jbrowse yet, we'll work on that when gene annotation is available.

We're going to put the project information inside the V2 reference genome assembly analysis and link to the vcf ... for now. Next steps:

• [ ] create a new analysis type for genotyping experiments
• [ ] create our first instance for j. regia and describe this experiment
• [ ] investigate LAS modules for genotype such as :
  • https://github.com/UofS-Pulse-Binfo/genotypes_loader
  • https://github.com/UofS-Pulse-Binfo/nd_genotypes
  • https://github.com/UofS-Pulse-Binfo/vcf_filter
  • https://github.com/UofS-Pulse-Binfo/kp_germplasm