Unaligned sequence for the human genome
The UCSC downloads site for human genome sequence includes unaligned sequence data (both "random" and "chrUn".). For completeness, we include these sequences in our indexed, reference genome. In order to use GATK, we have to resort the chromosome order and reindex the genome. However, we are unsure where to place the unaligned sequence in the chromosome order to make GATK happy.
How have these additional sequences been handled at the Broad?