CN-LoH analysis

[pbiology]

Need

• LOH in Scout from balsamic data (Myeloid panel) #1009

Suggested approach

LOH analysis was performed using the PON generated from the normal samples and results were presented. Further investigation, aiming to improve the method, lead to the identification of feature addition and improvements given in the sections below.

Considered alternatives

Were there alternative approaches which has been rejected?

Can be closed when

• The containers are added
  • feat: add cnvkit container #1252
  • feat: add purecn container #1255
  • feat: add htslib container #1234
• The CN-LOH is added to the TGA workflow
  • feat: add LOH analysis to TGA workflow #1278
• The CN-LOH is added to the report and uploaded to Scout
• Create a CNV report for TGA #1140

[khurrammaqbool]

The following PONs will Imrove LOH analysis:

• SNV
  • https://github.com/Clinical-Genomics/BALSAMIC/issues/1115
  • https://github.com/Clinical-Genomics/BALSAMIC/issues/1135
• CNV
  • Add PureCN PON

The following features will help with the interpretation of CN-LOH results:

• Gens for TGA workflow
• LOH-plots

The following features will further improve the analysis of CN-LOH:

• Update Sentieon #1235
• Restructuring core alignment workflow #1109
• Add pre-annotation blacklist filtering #1132
• feat: core pipeline restructuring  #1176
• Germline somatic variant calling best practices and filtration.
• Add TNScope to TGA workflow
• Improve the panel design

[pbiology]

Good refinement of the issue!
Could we open new issues for all of the improvement features suggested?