Filtering strategy

[fevac]

Need

We should improve the filtering strategy for SVs, ideally with soft-filtering whenever possible.

We have many open issues regarding this. We should add these changes or close these issues if not relevant:

SNVs/Indels

• Sentieon filters: https://github.com/Clinical-Genomics/BALSAMIC/issues/1258
• Variant in normal: https://github.com/Clinical-Genomics/BALSAMIC/issues/1254
• Max AF: https://github.com/Clinical-Genomics/BALSAMIC/issues/1180 and https://github.com/Clinical-Genomics/BALSAMIC/issues/1166
• Pathogenic; germline: https://github.com/Clinical-Genomics/BALSAMIC/issues/1256

SVs

• Refine maxDepth filtering: https://github.com/Clinical-Genomics/BALSAMIC/issues/1161
• Triallelic sites: https://github.com/Clinical-Genomics/BALSAMIC/issues/1293
• Rescue variants (too vague): https://github.com/Clinical-Genomics/BALSAMIC/issues/1133
• Exclusion list (too vague): https://github.com/Clinical-Genomics/BALSAMIC/issues/1132
• Reduce number of variants and technical artifacts: https://github.com/Clinical-Genomics/BALSAMIC/issues/1131 and https://github.com/Clinical-Genomics/BALSAMIC/issues/1316

UMI workflow

• Reduce number of variants: https://github.com/Clinical-Genomics/BALSAMIC/issues/1149

Suggested approach

A few sentences about the intended solution

Considered alternatives

Were there alternative approaches which have been rejected?

Requests/suggestions/bugs solved by the feature

Link any feature requests/bug reports or other issues which this would solve

Can be closed when

Link the issues needed to be closed for this to be implemented

Infrastructure changes

Create/Link issues in cg or servers needed for this feature

Blockers

Anything preventing this from happening?

[pbiology]

This was created as a meta-issue for voting in the pitch round. Let's close this as there are sub-stories for all