Reference Sequence Comparison

We want assess whether reference choice impacts alignment quality and variant calling for DRAGEN and Oncoanalyser pipeline.

• documentation to generate data
  • 1 Build Dragen reference
  • 2 Dragen aligment
  • 3 Run Oncoanalyser
  • 4 Analysis
• relevant output data
• scripts to make figure
• presentation for progress summary

ICAV2

pipeline will be launch from ICAV2 to connect

icav2 tenants enter umccr-prod
icav2 projects enter hmf-reference-testing-dev

to gain aws credential

icav2 projectdata temporarycredentials /quentin/ \
  --output-format=json | \
jq --raw-output \
  '
    .awsTempCredentials |
    [
      "export AWS_ACCESS_KEY_ID=\"\(.accessKey)\"",
      "export AWS_SECRET_ACCESS_KEY=\"\(.secretKey)\"",
      "export AWS_SESSION_TOKEN=\"\(.sessionToken)\""
    ][]
  '