Changes between Initial Version and Version 1 of net.sf.basedb.reggie/notes451


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Timestamp:
Jan 8, 2024, 9:18:51 AM (4 months ago)
Author:
Nicklas Nordborg
Comment:

Created update notes for Reggie 4.51

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  • net.sf.basedb.reggie/notes451

    v1 v1  
     1= Updating to Reggie 4.51 =
     2
     3== Support for EPICv2 ==
     4
     5The following changes are required for supporting EPICv2.
     6 
     7 * 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.
     8 * Use a batch importer to set `BeadChipType=EPICv1` on existing methylation items (assuming to no items are using the EPICv2 chip yet).
     9 * `reggie-config.xml` need to be updated with settings that are specific for each chip type. See [7509] for an example.
     10 * `reggie-config.xml` need to be updated to use the new container: `methylation-beta-v2-minfi1.48.sif`
     11 * Create a new software item for the methylation analysis.
     12
     13== Updated WGS variant calling pipeline ==
     14
     15 * `reggie-config.xml` need to be updated to use the new container: `/wgs-variantcall-v2-gatk.4.4.sif`
     16 * Create a new software item for WGS variant calling.
     17 * Existing variant call items should be deleted.
     18
     19