In 2019-2020, consequence prediction for repeat expansion variants was implemented via a bespoke pipeline, not going through VEP and using a limited set of consequence terms (short tandem repeat & trinucleotide). We should review the reasons for this decision (refer e.g. to minutes), discuss pros/cons of this strategy vs. unifying consequence prediction in VEP, and implement any necessary changes
In 2019-2020, consequence prediction for repeat expansion variants was implemented via a bespoke pipeline, not going through VEP and using a limited set of consequence terms (short tandem repeat & trinucleotide). We should review the reasons for this decision (refer e.g. to minutes), discuss pros/cons of this strategy vs. unifying consequence prediction in VEP, and implement any necessary changes