|Version 1 (modified by 4 years ago) ( diff ),|
Updating to Reggie 4.26
A. Before updating Reggie
1. Install a new Picard version on the prime cluster
We need Picard version 2.22.3 or higher since it fixes a problem with NovaSeq data files and the CheckIlluminaDirectory
function. Verify that the
reggie-config.xml is poiting to the correct installation directory
and modify if needed. Picard can be downloaded from https://github.com/broadinstitute/picard/releases.
B. Update Reggie
Update Reggie to version 4.26 as usual. Do not forget to run the Installation wizard.
C. After updating Reggie
1. Upload CTG sample sheet template
CTG_SampleSheet.xlsx file to the
/home/SCANB/Templates directory in BASE.
2. Import variant annotations
In the RNA library preparation and analysis/Variant calling pipeline section, run the Import variants for existing variant call raw bioassays wizard. This wizard will import variants that are found in some interesting genes as annotations to existing raw bioassay items and will take several minutes to run. The same functionality is included in the regular variant calling script so the wizard is not needed in the future. See #1229 for more information.