Removes the Support category, and the in silico tools we were using (MutationTaster, Polyphen, Sift, CADD, REVEL)
AlphaMissense takes a more substantial role (e.g. as a supporting element in Cat 2)
AlphaMissense scoring threshold doesn't change, but by default it becomes present on the naughty step these categories require a phenotype match list
If after MOI testing a variant is:
unsupported in a comp-het
isn't in a gene on a phenotype- or cohort-forced panel
all assigned categories are on the naughty step
we remove it from the analysis
Testing
needs testing, but first I need to downgrade my Java installation as JRE 21 doesn't support Spark, so Hail breaks
Checklist
[x] Related Issue created
[x] Tests covering new change
[x] Linting checks pass
Pretty substantial other change - the Dockerfile base is changed from the CPG AR driver image to a hail-genetics base. Shaves off almost 4GB from the build. Should be fine as we don't invoke gcloud/gsutil directly
Fixes
Proposed Changes
these categories require a phenotype matchlistTesting
needs testing, but first I need to downgrade my Java installation as JRE 21 doesn't support Spark, so Hail breaks
Checklist
Pretty substantial other change - the Dockerfile base is changed from the CPG AR driver image to a hail-genetics base. Shaves off almost 4GB from the build. Should be fine as we don't invoke gcloud/gsutil directly