Instead of a homebrewed extended-pedigree file unique to this application, switch over to using a GA4GH protocol compliant object for storing phenotype data
Adapter for shifting the ePED format into PED & Phenopackets
Removes the Pedigree generation module
Removes the in-Hail subsetting of the Pedigree (to leave only cols 1-6 for the de novo checker)
adds a new early checkpoint in Hail to fight the latest failure mode
Harmonises all the ArgParse CLI to mainly use input and output, along with some clarification about which panel file is needed
Fixes
Proposed Changes
inputandoutput, along with some clarification about which panel file is neededChecklist