This is a wrapper node for RealignerTargetCreator and the IndelRealigner walker of the Genome Analysis Toolkit (GATK). The aim of the node is to perform a realignment around putative insertions and deletions in a BAM file to reduce mapping errors and to avoid false positive variant calls. This is achieved in two steps. First, the RealignerTargetCreator walker generates a list of candidate regions for realignment. In the second step the IndelRealigner performs the realignment for all candidate regions. To increase the accuracy of realignment both walkers can be provided with sites of known indels. For further information, see the GATK documentation of the RealignerTargetCreator and the IndelRealigner.
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