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How bad will happen if I didn't feed known sites for IndelRealigner?
I think feeding known sites is just optional for the previous version of TargetCreator and IndelRealigner. But I don't know how strictly the local realignment step of GATK 2.0 require known sites. If things will dramatically go wrong due to lacking of known sites?
As you said below, "In the variant calling pipeline, the only tools that do not strictly require known sites are UnifiedGenotyper and HaplotypeCaller."
If there is also a statistical model only works with known sites for the local alignment step like quality recalibration?