This article is part of the workflow documentation describing the Best Practices for Variant Discovery in RNAseq data. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow.
Many variant callers specialize in either SNPs or Indels, or (like the GATK's own UnifiedGenotyper) have to call them using separate models of variation. The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region. In other words, whenever the program encounters a region showing signs of variation, it discards the existing mapping information and completely reassembles the reads in that region. This allows the HaplotypeCaller to be more accurate when calling regions that are traditionally difficult to call, for example when they contain different types of variants close to each other. It also makes the HaplotypeCaller much better at calling indels.
In addition, the HaplotypeCaller is able to correctly handle the splice junctions that make RNAseq a challenge for most variant callers. Specifically, HaplotypeCaller performs dangling head merging operations, and avoids using soft-clipped bases in order to minimize false positive and false negative calls. We also use lower confidence thresholds for calling variants on RNAseq. See the tutorial document for detailed parameter recommendations.