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Step order for PhaseBytransmission and ReadBackedPhasing
Hello GATK team,
Our lab is working on project involving exome sequencing for family trios and we were interested in determining the parent of origin for the trios. In one of the papers that we have come across, we found that the project team used ReadBackedPhasing first and then applied PhasedByTransmission.
I have read previous post on GATK forum and looked at the presentations which are provided by GATK team and found that the analysis is suggested to be done in a way where PhasedByTransmission step is done before ReadBackedPhasing. We are new to these tools, so if you could shed any light on how the tools work when combined, we would really appreciate it.
The step combinations which we have already have tried out are:
1) SelectVariants 2)ReadBackedPhasing 3)PhasedByTransmission
1) SelectVariants 2)PhasedByTransmission 3)ReadBackedPhasing