Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?