Changes between Version 4 and Version 5 of net.sf.basedb.reggie/notes432


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Timestamp:
Sep 16, 2021, 9:28:24 AM (3 years ago)
Author:
Nicklas Nordborg
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  • net.sf.basedb.reggie/notes432

    v4 v5  
    33**Note that BASE 3.19 is required for running Reggie 4.32.**
    44
    5 == A. Updated pipeline script ==
     5== A. Before updating Reggie ==
     6
     7=== 1. Updated pipeline script ===
    68
    79The `singlecolumnaverager.awk` script has been updated (see #1325). Install the new version at a suitable location and make sure to update reggie-config.xml with the new path.
    810
     11=== 2. Install VCF files for targeted genotyping ===
     12
     13VCF files (`dpyd.vcf`, `esr1.vcf` and `pik3ca.vcf`) for the targeted genotyping are in the http://onk-wiki.bmc.lu.se/svn/scanbprim/support-files/variant-calling/targeted repository and should be installed in the same location as the other databases used in the variant calling process. The VCF files need to be indexed by running the `index_all.sh` script. Finally, the `targeted-genotyping.toml` is a also a new file.
     14
     15
    916== B. Update Reggie ==
    1017
    11 Update Reggie to version 4.32 as usual. Do not forget to run the Installation wizard. This will create and fix several new annotations, etc. It will still complain about File server items that need to be manually configured:
     18Update Reggie to version 4.32 as usual, but note that several additions are needed in `reggie-config.xml` so a bit of preparation is maybe needed. Do not forget to run the Installation wizard. This will create and fix several new annotations, etc. It will still complain about File server items that need to be manually configured:
    1219
    1320  * !ImportGateway: This should be configured to access `lida1:/casa17/cmdtransfer` as the `scanb` user.
    … …  
    1724
    1825Also, a new entry `<step-1-import>` is needed since the first Trimmomatic step is different in the import pipeline.
     26
     27There are also several new configuration entries related to the targeted genotyping. See #1323.
     28
     29 * A new section `<targeted-genotyping>` defining the 3 currently existing targets: DPYD, ESR1 and PIK3CA
     30 * A new entry in the `<programs>` section is needed for `<gatk4>`.
     31 * Several new entries in the `<variant-call>` section.
     32   * `<vcfanno-options-targeted>`
     33   * `<snpeff-options-targeted>`
     34   * `<haplotypecaller-options>`
    1935
    2036== C. After updating Reggie ==
    … …  
    3147 * Create a new `Merging` software representing the FASTQ import variant that uses a different Trimmomatic first step. Annotate `MergeType=Import`, `Pipeline=RNAseq` and make it project default.
    3248
     49 * Create a new `Variant calling` software item. Annotate with `VariantCallType=TargetedGenotype` and make it the project default.
     50
    3351
    3452=== 3. Create or annotate protocol items ===
    … …  
    4462
    4563Pool aliquots created by the external sequencing wizard have incorrect names. See #1301.
     64
     65=== 5. Run the targeted genotyping analysis for all existing variant calls ===
     66
     67The **Start targeted genotyping** wizard is in the **RNA library preparation and analysis** section inside the **Secondary analysis wizards** box.