wiki:net.sf.basedb.reggie/notes451

Updating to Reggie 4.51

Support for EPICv2

The following changes are required for supporting EPICv2.

  • The BeadChipType annotation has changed the Epic850K value to EPICv1 and added EPICv2. Existing bead chip items need to be updated with a batch import.
  • Use a batch importer to set BeadChipType=EPICv1 on existing methylation items (assuming to no items are using the EPICv2 chip yet).
  • reggie-config.xml need to be updated with settings that are specific for each chip type. See [7509] for an example.
  • reggie-config.xml need to be updated to use the new container: methylation-beta-v2-minfi1.48.sif
  • Create a new software item for the methylation analysis.

Updated WGS variant calling pipeline

  • reggie-config.xml need to be updated to use the new container: /wgs-variantcall-v2-gatk.4.4.sif
  • Create a new software item for WGS variant calling.
  • Existing variant call items should be deleted.

Last modified 3 months ago Last modified on Jan 8, 2024, 9:18:51 AM
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