UnifiedGenotyper behaving differently when supplied with single or multiple bam files
Posted in Ask the team | Last updated on 2012-10-18 01:09:20


Comments (8)

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:

GT:AD:DP:GQ:MQ0:PL 1/1:0,66:66:99:0:2337,187,0

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

Gene


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