[User Story] Remove low-mappability variants from gnomad vcf used for GENS

[mathiasbio]

Need

As a clinician I want noiseless BAF profiles in GENS, but primarily as a bioinformatician I want to reduce manual work by needing to manually run DNAscope with the given gnomad where problematic regions have been filtered out. See issue: #1431

Suggested approach

We can filter out variants in low-mappability regions of the current gnomad VCF used for GENS BAF plot creation and replace the current gnomad VCF in production with this filtered VCF. This should hopefully remove the risk of cases crashing in production due to memory, and beyond that it's good practice to remove these regions from analysis.

Considered alternatives

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Deviation

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System requirements assessed

• Yes, I have reviewed the system requirements

Requirements affected by this story

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Risk assessment needed

• Needed
• Not needed

Risk assessment

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SOUPs

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Can be closed when

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Blockers

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Anything else?

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