Using UnifiedGenotyper on single chromosome without coordinates

Question

[shpak.max]

I have a large number of bam files, containing subsets that were aligned against (slightly) different reference genomes that were created to account for differences in indel distributions etc across different populations.

I am specifically interested in genetic variation in the X chromosome (corresponding to contig 4 in the assembly), so I attempted to run GATK's UnifiedGenotyper using the argument

-L 4:

without coordinates (because, as described above, the coordinates for this chromosome differ slightly from sample to sample. Running UnifiedGenotyper with this argument (both with and without the ":") returns an error and terminates.

Is there some way to restrict UnifiedGenotyper to a single chromosome/contig without specifying the coordinates?