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IndelRealigner results are different at time
I use GATK v2.3 Lite.
I found that the output bam files generated by IndelRealigner from an input bam file were different at time.
There were only 4 realigned reads at a certain position at the first trial, but the realigned reads increased to 5 at the second trial.
Finally, it affected the variant calls.
Is there any random sampling process along the IndelRealigner ?
Could you explain more about the algorithm of IndelRealigner?