Using UnifiedGenotyper on single chromosome without coordinates
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
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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