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

Timestamp:

Jan 28, 2020, 7:50:40 AM (5 years ago)

Author:

Nicklas Nordborg

Comment:

Added note about updating to Reggie 4.25

net.sf.basedb.reggie/notes425

@@ +1 @@
+= Updating to Reggie 4.25 =
+
+
+== 1. New/updated pipeline scripts ==
+
+There are new pipeline scripts: http://baseplugins.thep.lu.se/browser/other/pipeline/trunk
+Download and install at a suitable location on the prime cluster:
+
+ * `mut_stats.py`
+ * `mutation_signature.R`
+ * `Rscript.sh`
+
+== 2. New databases for annotating variants ==
+
+The following databases have been updated:
+
+ * dbSNP to version 153
+ * COSMIC to version 90
+ * gnomAD to version 2.1.1
+ * Swegen to version 20180409
+
+The other databases are the same as before. The database update also affect some of the other configuration files.
+Everything that is needed can be found at `casa4:/disk/lv-p822a-50tb-b/thep-nni/vcall/newdbs`. All files and 
+subdirectories should be copied to a new location in the "references" directory in the Prime cluster, for example,
+`prime:/disk/reference/scanb/rnaseqvarcall-feb2020`.
+
+Change the configuration `<variant-call><base-dir>` setting in `reggie-config.xml` to point to the new location of
+the databases.
+
+== 3. 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.
+The wizard need to create two databases, one with tumor samples and one with normal samples. This may take a few hours.
+Databases will be saved in the temporary job directory (the exact path is printed in the job information afterwards)
+and need to moved to the database-directory manually, eg. prime:/disk/reference/scanb/rnaseqvarcall-feb2020/scanb
+
+Note that both databases should be stored in the same directory, and make sure that they have correct names:
+
+ * `scanb-tumors.vcf.gz` (and a corresponding .tbi file)
+ * `scanb-normals.vcf.gz` (and a corresponding .tbi file)
+
+
+ 
+
+