Complete task 4.3.1 “Joint cohort variant genotyping” (meta-issue)

[tskir]

• [x] Complete outstanding technical actions
  • [x] #14 Verify that memory requirements work
  • [x] #17 Verity that packages are installed in the Nextflow pod
• [x] Documentation
  • [x] #25 Rearrange the docs to separate general approach and workflow specific details
  • [x] #26 Write joint cohort genotyping documentation
  • [x] #27 Expand the docs to better establish context
• [x] Pipeline
  • [x] #29 Decide on the reference datasets
  • [x] #28 Find/write the demonstrator genotyping pipeline
  • [x] #30 Test and debug the pipeline
  • [x] #31 Find out about TESK deployment at EBI
• [x] Milestone
  • [x] #32 Fill in the milestone slide
  • [x] #33 Write the milestone report

[tskir]

• Decided to use two environments: CSC TESK + EBI LSF
• Decided to use two datasets: EGA synthetic dataset + GIAB