The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
I am using PhaseByTransmission to phase variants called from a trio (mother, father and son) contained in a VCF file. It's my first time using this tool. Do I need to follow any convention when naming my samples? Do the sample names in the VCF file need to match the Family ID, the individual ID, or a combination of the two in the PED file? Do they need to be in the same order?