Annotate SNVs and SVs with Somatic and Germline observation frequencies from LoqusDB

[khurrammaqbool]

Need

Somatic SNV and SV variant observation frequencies DB using LoqusDB started to populate since release of BALSAMIC v11. Next step is to add annotation feature of the SNV and SV observation frequencies in BALSAMIC before implementation of the filtration against the somatic variant observation frequencies.

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

• [x] BALSAMIC annotates Clinical SNVs with loqusdb germline SNV Frequencies
• [x] BALSAMIC annotates Clinical SNVs with loqusdb somatic SNV Frequencies
• [x] BALSAMIC annotates Clinical SVs with loqusdb somatic SV Frequencies
• [x] Exported variants (https://github.com/Clinical-Genomics/BALSAMIC/issues/1318)
• [x] Updated documentation

Blockers

Anything preventing this from happening?

[khurrammaqbool]

TNScope does not include GQ in the FORMAT field of the VCF, which is required by loqusDB. This is fixed in loqusDB https://github.com/Clinical-Genomics/loqusdb/issues/117. The database will be re-build after testing.

[khurrammaqbool]

Annotation for SNVs, somatic observation frequencies are added in https://github.com/Clinical-Genomics/BALSAMIC/pull/1187. The next step for the annotation will be to export databases and link then in cg with BALSAMIC.

[khurrammaqbool]

Annotation for SVs, somatic observations frequencies will be added in https://github.com/Clinical-Genomics/BALSAMIC/issues/1193