GATK VQSR on indels
Are there any precautions to be taken before applying VQSR to an "INDEL" VCF?
meaning, how does the algorithm inside VQSR recognize whether an indel in the input VCF is the
same as in the training dataset?
Is there some re-alignment, or equivalent representation to be done on either the input VCF,
training VCF or both prior to running the VCF through the VQSR command line?