BALSAMIC v12.0.0 release

[khurrammaqbool]

Balsamic features for the next release:

Balsamic v12

Alignment

• [ ] #993 :
  • [ ] Adapt the CLI to accept multiple reads and concatenate the fastqs
  • [ ] Remove concatenation and merge aligned BAM in BALSAMIC

Annotation

• [ ] loqusdb tumor SNV Frequencies for WGS:
• [ ] loqusdb tumor SV Frequencies for WGS:
• [ ] loqusdb somatic SNV Frequencies for WGS:
• [ ] loqusdb somatic SV Frequencies for WGS:
• [ ] Update documentation

Filtering strategy prior to upload to Scout

• [ ] Add Pre-annotation blacklist filtering:
• [ ] Implement filtering against loqusdb tumor and somatic observations:
• [ ] Update documentation

Rescue filtered out variants:

• [ ] Add Filter PASS:
• [ ] Update documentation

Variant callers

• [ ] Add CNVpytor for WGS T-N analysis
• [ ] Update documentation

PON

• [ ] Add TNhaplotyper PON :
• [ ] Generate a panel of normal reference and use it as input for BALSAMIC analysis
• [ ] Update documentation

Scout

• [ ] Add CNVpytor TN analysis PDF to Scout:

Update delivery report

• [ ] Delivery report for QC only analysis
• [ ] Update documentation

File delivery

• [ ] Update stored and delivered files (HERMES & CG)
• [ ] Update documentation
• [ ] Update atlas

Feature Update

• [ ] Version information regarding tools and databases used in analysis
• [ ] Update cluster.json for cpu, time for all the rules
• [ ] Add memory in cluster.json
• [ ] Split BAM for non-threaded processes

Bug Fixes

• [ ]

Timeline:

To be defined.

[ivadym]

Isn't it trivial to have this issue if we have a v12 milestone?

Any thoughts @Clinical-Genomics/cancer-bioinfo?

[pbiology]

Isn't it trivial to have this issue if we have a v12 milestone?

Any thoughts @Clinical-Genomics/cancer-bioinfo?

I agree that we can use the milestone to keep track of what will go into the v12 release. However, we shouldn't lose track of the items listed in bullet points here.

[pbiology]

Feature issues are now created for what I hope is all parts of this issue:

• 1130

• 1131

• 1132

• 1133

• 1134

• 1135

• 1136

• 1137

• 1138

• 1139

With these tracked in https://github.com/orgs/Clinical-Genomics/projects/46 I think we can close this issue

[ivadym]

Nice! Since everything here has been included in the board I will close this issue