Updating to Reggie 4.32

Note that BASE 3.19 is required for running Reggie 4.32.

A. Before updating Reggie

1. Updated pipeline script

The 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.

2. Install VCF files for targeted genotyping

VCF 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.

B. Update Reggie

Update 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:

• ImportGateway: This should be configured to access lida1:/casa17/cmdtransfer as the scanb user.
• ImportArchive: This should be configure to access lida1:/casa17/project_archive/import_archive/ as the scanb user.

The same paths also need to be specified in the reggie-config.xml file in <import-gateway> and <import-archive> settings.

Also, a new entry <step-1-import> is needed since the first Trimmomatic step is different in the import pipeline.

There are also several new configuration entries related to the targeted genotyping. See #1323.

• A new section <targeted-genotyping> defining the 3 currently existing targets: DPYD, ESR1 and PIK3CA
• A new entry in the <programs> section is needed for <gatk4>.
• Several new entries in the <variant-call> section.
  • <vcfanno-options-targeted>
  • <snpeff-options-targeted>
  • <haplotypecaller-options>

C. After updating Reggie

1. Change existing software items

• All Demuxing software should be annotated with DemuxType=Picard
• All Merging software should be annoteted with MergeType=Default

2. Create new software items

• Create a new Demuxing software representing the bcl2fastq demuxing that is done by CMD. Annotate DemuxType=bcl2fastq, Pipeline=RNAseq, ExternalRef=bcl2fastq and make it project default.

• 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.

• Create a new Variant calling software item. Annotate with VariantCallType=TargetedGenotype and make it the project default.

3. Create or annotate protocol items

We either need to create new protocol items or annotate existing protocol items with ExternalRef so that they can be referenced in imports from CMD.

• Library preparation
• Allprep extraction (3 variants for RNA, DNA and FlowThrough)
• Sample handling

4. Fix pool aliquot names

Pool aliquots created by the external sequencing wizard have incorrect names. See #1301.

5. Run the targeted genotyping analysis for all existing variant calls

The Start targeted genotyping wizard is in the RNA library preparation and analysis section inside the Secondary analysis wizards box.