I am attempting to run GATK's PhasebyTransmission command to phase a vcf file contains a father, mother, son trio generated from complete genomics mkvcf command.
After creating the ped file and running the command I generate the error: "MESSAGE: BUG: Attempted to get likelihoods as strings and neither the vector nor the string is set!". I am not exactly sure what this means.
When I check my file and the documentation I am able to see that the 'GL' field is contained in the file, but could this not be the case? I have attached a few lines from the vcf I am using.
Any help with resolving the this issue would be of great help.