Changes between Version 1 and Version 2 of net.sf.basedb.reggie/notes425

Timestamp:

Jan 31, 2020, 8:29:57 AM (4 years ago)

Author:

Nicklas Nordborg

Comment:

Update the release notes for Reggie 4.25

net.sf.basedb.reggie/notes425

@@ -1 +1 @@
 = Updating to Reggie 4.25 =
 
+== A. Before updating Reggie ==
 
-== 1. New/updated pipeline scripts ==
+=== 1. Disable the Variant calling pipeline ===
+
+Disable auto-confirmation for the variant calling by setting `AutoProcessing=Disable` on
+the **Variant Calling Pipeline** item list.
+
+=== 2. Install new/updated pipeline scripts ===
 
 There are new pipeline scripts: http://baseplugins.thep.lu.se/browser/other/pipeline/trunk
@@ -11 +17 @@
  * `Rscript.sh`
 
-== 2. New databases for annotating variants ==
+=== 3. Install new databases for annotating variants ===
 
 The following databases have been updated:
@@ -28 +34 @@
 the databases.
 
-== 3. Create new SCAN-B databases ==
+== B. Update Reggie ==
+
+Update Reggie to version 4.25 as usual. Do not forget to run the Installation wizard.
+
+== C. After updating Reggie ==
+
+=== 1. Create new SCAN-B databases ===
 
 Use the new Reggie wizard (Build SCAN-B variant database) to create new databases for the existing SCAN-B samples.
@@ -40 +52 @@
  * `scanb-normals.vcf.gz` (and a corresponding .tbi file)
 
+=== 2. Test the variant calling pipeline ===
+
+The annotation and filtering part of the variant calling pipeline can now be tested. Select some alignments that already have raw variant calls.
+
+=== 3. Enable the Variant calling pipeline ===
+
+Enable auto-confirmation for the variant calling by removing `AutoProcessing=Disable` from
+the **Variant Calling Pipeline** item list.
+
+=== 4. Complete the annotation and filtering step for all alignments that already have raw variant calling ===