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


Ignore:
Timestamp:
Jan 31, 2020, 8:29:57 AM (4 months ago)
Author:
Nicklas Nordborg
Comment:

Update the release notes for Reggie 4.25

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  • net.sf.basedb.reggie/notes425

    v1 v2  
    11= Updating to Reggie 4.25 =
    22
     3== A. Before updating Reggie ==
    34
    4 == 1. New/updated pipeline scripts ==
     5=== 1. Disable the Variant calling pipeline ===
     6
     7Disable auto-confirmation for the variant calling by setting `AutoProcessing=Disable` on
     8the **Variant Calling Pipeline** item list.
     9
     10=== 2. Install new/updated pipeline scripts ===
    511
    612There are new pipeline scripts: http://baseplugins.thep.lu.se/browser/other/pipeline/trunk
     
    1117 * `Rscript.sh`
    1218
    13 == 2. New databases for annotating variants ==
     19=== 3. Install new databases for annotating variants ===
    1420
    1521The following databases have been updated:
     
    2834the databases.
    2935
    30 == 3. Create new SCAN-B databases ==
     36== B. Update Reggie ==
     37
     38Update Reggie to version 4.25 as usual. Do not forget to run the Installation wizard.
     39
     40== C. After updating Reggie ==
     41
     42=== 1. Create new SCAN-B databases ===
    3143
    3244Use the new Reggie wizard (Build SCAN-B variant database) to create new databases for the existing SCAN-B samples.
     
    4052 * `scanb-normals.vcf.gz` (and a corresponding .tbi file)
    4153
     54=== 2. Test the variant calling pipeline ===
     55
     56The annotation and filtering part of the variant calling pipeline can now be tested. Select some alignments that already have raw variant calls.
     57
     58=== 3. Enable the Variant calling pipeline ===
     59
     60Enable auto-confirmation for the variant calling by removing `AutoProcessing=Disable` from
     61the **Variant Calling Pipeline** item list.
     62
     63=== 4. Complete the annotation and filtering step for all alignments that already have raw variant calling ===
    4264
    4365