Somatic impact scores

[pbiology]

Need

BALSAMIC adds SOMATICSCORE to the final SV VCF (*.clinical.filtered.pass.vcf.gz). This final VCF file is then uploaded to scout. SCOMATICSCORE is computed by manta for tumor-normal cases.

Suggested approach

A few sentences about the intended solution

Considered alternatives

Were there alternative approaches which has been rejected?

Can be closed when

• https://github.com/Clinical-Genomics/scout/issues/3883
• https://github.com/Clinical-Genomics/scout/issues/3884

Blockers

Anything preventing this from happening?

[khurrammaqbool]

The following Issues are opened in Scout requesting to add and filter SOMATICSCORE for SVs from tumor-normal cases.

• add SOMATICSCORE for SVs
• Filter by SOMATICSCORE

[khurrammaqbool]

@mathiasbio would you like to add to the SOMATCSCORE described above and the associated action points?

[mathiasbio]

I will take a look!

[pbiology]

The development on the BALSAMIC side is completed and the final part is on the Scout side.

[khurrammaqbool]

Added to Scout in https://github.com/Clinical-Genomics/scout/commit/a21b6f60721a644aaff134b31962fdf8f896164e

[khurrammaqbool]