I am sorry that we figured the issue is in the vep_cache folder. We have vep installed on AWS cluster and local cluster. And this folder has discrepancy, when we used the VEP output from local to compare to the mt file generated in the cluster which misleads us to HAIL function. We figured out the problem when we logged into the cluster EC2. We were supposed to fetch the logs file you required on the EC2 and we discovered the issue. Those EC2 instances are instantiated on-demand for a cluster and it is not easy to access. Thatās why we didnāt really check the VEP there directly before. I would like to appreciate your help and I had a lot of take-aways from you reply!
Glad youāve got a fix! I can sympathize with VEP struggles ā weāve had many over the years.
Iām also glad thereās not some cryptic Hail JSON parsing bugā¦