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SACGF / variantgrid

VariantGrid public repo
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gnomADv4 common filter #1119

Open davmlaw opened 1 month ago

davmlaw commented 1 month ago

We are still using 3.1 for GRCh38, haven't generated one for new gnomAD 4

Code currently dies looking for this version, which means installing from scratch no longer works

Need to create a v4 GRCh38 gnomad AF file and alter pipelines

See:

settings.VCF_IMPORT_COMMON_FILTERS

Make sure you put the gnomAD version in the name (unlike last one)

davmlaw commented 1 month ago

Not user testable

Added to deployment check - when upgrading systems should get a notice to download it if not there (and Copied to variantgrid.com - so available for download)

davmlaw commented 1 month ago

Thinking about it, we should only do this optimisation when the common filter gnomAD version equals the analysis gnomAD version - we should do an explicit check

This is stored in an object CohortGenotype.CohortGenotypeCommonFilterVersion

Maybe even expose that somewhere eg in node debug tab

The place to where it's set is:

analysis.models.nodes.analysis_node.AnalysisNode.get_annotation_kwargs

The place that it's tested and decide what CGC to include is:

snpdb.models.models_cohort.CohortGenotypeCollection.get_annotation_kwargs