= 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.