I just created a bed file from the GATK walker VariantsToBinaryPed. It was of course supposed to be a ped file. Now I can't use it as input to phaseByTransmission. My question is: is the file crap even if I change the file ending afterwards? If so, are all filetypes so sensitive?
And while I'm at it, an irrelevant bonus question: has anyone tried phaseByTransmission with more than a trio?
Edit: my problem was the `-ped` option. It was typed `-bed`. I'm having troubles typing ped here as well. My brain is telling me to go to sleep.