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?
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