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I was running UnifiedGenotyper on a set of 26 bam files. There was one particular position where I was comparing calls to the actual pileup and I noticed a major discrepancy. There was a no-call ("./.") for that position for one of the bam files while most other samples had calls. That non-called sample, though, had a very convincing variant in the pileup, with lots of high quality coverage at that position.
I then tried running just that bam file alone through UnifiedGenotyper, or that bam file along with two others. In both cases, the 1/1 variant is called properly with the following genotype field:
This seems to me to be a serious bug. Is this anything that's been noted before?
I am running GATKLite version 2.1-3-ge1dbcc8