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.
PhaseByTransmission with more than just trio
Is it possible to use PhaseByTransmission with families that are larger than a single trio? I have a family with four siblings. If I include all of the siblings in the PED I get:
PhaseByTransmission - Caution: Family BMD has 6 members; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped. ERROR MESSAGE: Bad input: No PED file passed or no trios found in PED file. Aborted.
And if I just include the one key trio with the proband, I get the following:
ERROR MESSAGE: Sample BMD006_R found in data sources but not in pedigree files with STRICT pedigree validation
There does not seem to be an accessible argument for relaxing the pedigree validation. Is there a way to use PhaseByTransmission with my larger family?