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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?

Thank you!



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