I notice that although UnifiedGenotyper and HaplotypeCaller identify indels, none or reported greater than a length of around 50bp. Obviously integrating this ability into the already complicated algorithms is not easy, nor are such variants especially common - but they can easily be biologically-important, as well as interfered SNP calls, e.g. if a SNP is in a heterozygous deletion.
Do you know of any callers for larger indels/CNVs, specifically for multi-sample NGS projects ? I've looked at pindel and break-dancer (and probably a few others) but they seem mostly for single samples.