Annotation included a whole genome MT -> VCF -> Annotation -> MT loop, despite results being filtered down to genic/gene panel in Hail stage
Proposed Changes
updates VEP image, references, annotation digestion to point to 110
removes dedicated sites only vcf generation - skips for VCF input, uses Hail for MT input
when generating new annotations from MT, uses gencode GTF file to region filter to genes +/-5000bp
Not sure that we really need this change, it was an offline experiment that got out of control. It does mean that we can do a minimal re-annotation of existing MTs without re-running the main pipeline to test out the AlphaMissense results
Fixes
whole genome MT -> VCF -> Annotation -> MTloop, despite results being filtered down to genic/gene panel in Hail stageProposed Changes
Not sure that we really need this change, it was an offline experiment that got out of control. It does mean that we can do a minimal re-annotation of existing MTs without re-running the main pipeline to test out the AlphaMissense results
Checklist