The "Download labels" button in the DNA/RNA/FlowThrough registration wizard doesn't work

[Nicklas Nordborg]

The "Download labels" is visible when there are lysates for re-extraction. New labels are needed for the DNA, RNA and FlowThrough tubes. Clicking on the button doesn't do anything and there are no error messages.

A workaround is to use the protocol wizard. The "Download labels" button is working on that page.

NOTE! Comments about "mBAF analysis" was added to this ticket by accident. They should belong to ticket #1068!

[Nicklas Nordborg]

(In [4907]) Fixes #1058: The "Download labels" button in the DNA/RNA/FlowThrough registration wizard doesn't work

[Nicklas Nordborg]

(In [5015]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

The installation wizard is now creating the "mBAF analysis" item list. Added "Start mBAF analysis" wizard to the start page (including a counter for the new item list). The Hisat auto-confirm and manual confirm is also adding items to the new list.

[Nicklas Nordborg]

(In [5029]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Started to implement the "Start mBAF analysis" wizard. It is possible to select alignments and finish the registration, but it doesn't currently do anything.

[Nicklas Nordborg]

(In [5030]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Started to implement the actual mBAF job creation implementation for submitting jobs to the cluster. It follows the same pattern as, for example, the StringTie implementation. So far it is an empty skeleton that doesn't actually create anything.

[Nicklas Nordborg]

(In [5032]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

A script for running HaplotypeCaller is now generated and submitted to the cluster. It seems to run as expected and result files are copied back to the same directory as the other alignment files. Nothing is imported back into BASE.

A configuration section has been added to reggie-config.xml. It is currently using the same VCF reference as the identity genotyping but this should be replaced by a full VCF in the future.

[Nicklas Nordborg]

(In [5033]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Files are now created in BASE and linked to the alignment.

[Nicklas Nordborg]

(In [5035]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Implemented auto-confirm for mBAF analysis. The implementation is similar to the auto-confirm for Gene/Pilot report. A temporary link between the alignment and job is created. If the job fails auto-confirmation will re-schedule the alignment for a new mBAF analysis.

[Nicklas Nordborg]

(In [5036]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

The auto-confirmation service was not notified by failed jobs. The implementation has been modified so that both the auto-confirmation and counter service gets a notification once a job has been completed. The auto-confirmation is waiting a short time to make sure that the transaction that is handling the job has time to commit and store everything in the database.

[Nicklas Nordborg]

(In [5037]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Auto-confirmation after Hisat alignment should now also start the mBAF analysis.

[Nicklas Nordborg]

(In [5039]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Added a quick parsing step that extracts the number of SNPs in total and passing filter.

[Nicklas Nordborg]

(In [5040]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Started with refactoring parsing of VCF files to make it easier to extract and analyze data that we are interested in.

[Nicklas Nordborg]

(In [5045]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Collecting statistics for each regions has now been implemented. Z-score and p-values are calculated by comparing average mBAF values to the normal reference.

[Nicklas Nordborg]

(In [5046]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Added 4 new annotation types for mBAF analysis:

• mBAF_SNPCount: Total number of SNPs that was found in the VCF files that has genotype data
• mBAF_SNPCountFiltered: Number of SNPs that passed the filter for being used in mBAF calculatations.
• mBAF_MinPValue: The lowest p-value for all regions
• mBAF_MinPRegion: The region with the lowest p-value.

[Nicklas Nordborg]

(In [5049]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Implemented a plotting function via R. mBAF statistics is exported to a temporary working directory and a R script is called which generates a plot in PNG format. The plot is uploaded to BASE and linked to the alignment as 'mbaf_genotype.png'.

[Nicklas Nordborg]

(In [5050]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Added two more mBAF-related annotations:

• mBAF_NumRegions: Number of regions that we have mBAF values for.
• mBAF_SignificantRegions: Number of regions that are significantally different from the normal references

[Nicklas Nordborg]

(In [5051]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Implemented a region filter that filters out regions with less than 20 SNPs.

Updated the plot function to not highlight regions below the limit. It can now also handle regions without data (eg. NA) values in the mBAF column.

[Nicklas Nordborg]

(In [5054]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Added a "mBAF plotter plug-in". It can be used to re-evaluate the mBAF information in existing VCF files and create a new plot and update the mBAF annotations on the alignment. The plug-in can be used in single-item and list contexts.

[Nicklas Nordborg]

(In [5056]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

The mBAF plotter now creates a single working directory so that the R script and reference only need to be copied once.

[Nicklas Nordborg]

(In [5057]) References #1058: Add mBAF analysis step to the Hisat/StringTie pipeline

Added a new software type Variant calling that can be used for this step. The VariantCallType annotation should be set to mBAF.