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Created 2013-06-07 18:45:10 | Updated 2013-06-07 18:45:59 | Tags: commandlinegatk phasebytransmission mkvcf
Comments (8)

Hello Team,

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.

Thank you

JumaQuar