Unexpected indel call
we observe an unexpected deletion call (GATK UnifiedGenotyper 3.0 and 2.5) in a setup with three samples called together. In the file call.txt you find the call. From the pileup (pileup.txt, position 19:57325555) we would expect, that the indel would only be called for the first sample.
Is there another source of information, that makes GATK believe, that the deletion also occurs in the second and third sample?
Thanks in advance,