VariantsToBinaryPed pedigree problem
Using GATK 2.8-1-g932cd3a, VariantsToBinaryPed seems to swap the Father and Mother ID columns when given an input .fam file. I've observed this with several different runs on different input sets.
The documentation for the --metaData flag suggests that this may happen. The docs give the .fam file column order as expected, but examining the example files provided inline, both swap the mother and father of NA12878: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_VariantsToBinaryPed.html
Thanks in advance for taking a look at this.