[User Story] Add more SV databases for frequency filtering

[mathiasbio]

Need

As a clinician I want true somatic variants, even when doing tumor only analyses without a matched normal.

Currently SV filtering is done with the swegen database and the locally built database of germline calls from the rare-disease pipeline. However these databases are likely not exhaustive and it could be beneficial to add more databases. In this article https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9047340/ they describe using several additional databases for SV filtering:

For population frequency-based filtering, we considered the variants occurring in more than 1% of the population as common. SVs called in the VCF file are removed from the analysis if they show greater than 80% reciprocal overlap with a common variant in any of the source databases (DGV, gnomAD-SV, dbSNP, and HGSVC SVs).

We should add these and see if they are useful in our filtering as well. In short, they mentioned these databases:

DGV: http://dgv.tcag.ca/dgv/app/home
gnomAD-SV: https://gnomad.broadinstitute.org/news/2019-03-structural-variants-in-gnomad/
HGSVC SVs: https://www.internationalgenome.org/data-portal/data-collection/structural-variation

And dbSNP (though I cannot find what they used)

Suggested approach

No response

Considered alternatives

No response

Deviation

No response

System requirements assessed

• Yes, I have reviewed the system requirements

Requirements affected by this story

No response

Risk assessment needed

• Needed
• Not needed

Risk assessment

No response

SOUPs

No response

Can be closed when

No response

Blockers

No response

Anything else?

No response