We ran a recent version of Haplotyper Caller on our SOLiD targeted resequencing data and got a ridiculous number of indels. We took a closer look at some and there was absolutely no evidence for an indel at a called position, and wondered whether the internal realignment was doing something weird? Is this a known problem for SOLiD data? Our Illumina data works much better. It makes us now wary of using GATK for SOLiD data...is it just a filtering thing?