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Is it useful to call LeftAlignIndels after IndelRealigner
In my pipeline to find variants in bacterial genome, I am first calling IndelRealigner and then calling variants using HaplotypeCaller. As left aligning of indels seems to be an important step, should I need to call LeftAlignIndels after the IndelRealigner?
I understand that documentation for LeftAlignIndels mentions that it is not required if using sophisticated tools like HaplotypeCaller, but I may be calling variants using other tools such as FreeBayes (just to compare variants found using different tools).
Thanks for reading and any help.