I just created a **b**ed file from the GATK walker VariantsToBinaryPed. It was of course supposed to be a **p**ed 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.
<p>Ha! This is a confusing question. The &quot;mansplainer&quot; in me wants to tell you that file extensions don&#39;t matter one bit, although in this case file extensions do matter, and some understanding of the file *format* is needed.</p>

<p>Most people will be familiar with .bed files as text files representing interval data. In your case, you are creating a <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#bed">binary version of a .ped</a> text file, which represents a pedigree for genetic analysis. Your .bed pedigree file does not equal other .bed interval files, so in this case the file extension is not only arbitrary but also confusing. Most importantly you *cannot* change the file extension from .bed to .ped and use the resulting file for software that expects the text representation of a pedigree.</p>
