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)