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Can probably eliminate sort in RealignIndels #1137
We have a sort in the INDEL realigner that takes most of the realignment time. We do this so that we can get the full alignment position of all reads that cover a target, but this is actually an unnecessary step, since we join the reads back later and just check for overlap. If we eliminate this, we should improve INDEL realignment runtime by ~60% with negligible impact on accuracy.
I'm thinking that I'll support this via a flag.
GATK and Freebayes handle indel realignment inside the variant caller, eliminating the extra realign indels step.
If the variant caller(s) that you plan to use with Adam also are haplotype aware this would mean that you could drop the indel realignment step/tool.