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


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Timestamp:
Jan 28, 2020, 7:50:40 AM (2 years ago)
Author:
Nicklas Nordborg
Comment:

Added note about updating to Reggie 4.25

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  • net.sf.basedb.reggie/notes425

    v1 v1  
     1= Updating to Reggie 4.25 =
     2
     3
     4== 1. New/updated pipeline scripts ==
     5
     6There are new pipeline scripts: http://baseplugins.thep.lu.se/browser/other/pipeline/trunk
     7Download and install at a suitable location on the prime cluster:
     8
     9 * `mut_stats.py`
     10 * `mutation_signature.R`
     11 * `Rscript.sh`
     12
     13== 2. New databases for annotating variants ==
     14
     15The following databases have been updated:
     16
     17 * dbSNP to version 153
     18 * COSMIC to version 90
     19 * gnomAD to version 2.1.1
     20 * Swegen to version 20180409
     21
     22The other databases are the same as before. The database update also affect some of the other configuration files.
     23Everything that is needed can be found at `casa4:/disk/lv-p822a-50tb-b/thep-nni/vcall/newdbs`. All files and
     24subdirectories should be copied to a new location in the "references" directory in the Prime cluster, for example,
     25`prime:/disk/reference/scanb/rnaseqvarcall-feb2020`.
     26
     27Change the configuration `<variant-call><base-dir>` setting in `reggie-config.xml` to point to the new location of
     28the databases.
     29
     30== 3. Create new SCAN-B databases ==
     31
     32Use the new Reggie wizard (Build SCAN-B variant database) to create new databases for the existing SCAN-B samples.
     33The wizard need to create two databases, one with tumor samples and one with normal samples. This may take a few hours.
     34Databases will be saved in the temporary job directory (the exact path is printed in the job information afterwards)
     35and need to moved to the database-directory manually, eg. prime:/disk/reference/scanb/rnaseqvarcall-feb2020/scanb
     36
     37Note that both databases should be stored in the same directory, and make sure that they have correct names:
     38
     39 * `scanb-tumors.vcf.gz` (and a corresponding .tbi file)
     40 * `scanb-normals.vcf.gz` (and a corresponding .tbi file)
     41
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     43 
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