Meaning does it matter if my intervals file goes chr1, chr10, instead of chr1, chr2 ? Additionally, will a command line error occur if bam files are not sorted in coordinate order with respect to the reference?
Yes, it matters. The order must exactly match the official reference canonical ordering. You cannot have lexicographical sorting.
An error will be thrown if the bam is not sorted in order of the reference.
Please see this article for more information: http://gatkforums.broadinstitute.org/discussion/1204/what-input-files-does-the-gatk-accept-require
Great thanks Sheila!