Is it worth to consider Realigned & Recaliberated bam file for further Pindel Analysis...?

Hi,

I have gone through the Realignment step and found Re aligner will change the CIGAR of alignment in bam file.
Most of the structaral variant detection tool dependent upon CIGAR field. So my question is it right to consider re calibrated bam file, does it has any advantage for SV Detection over Raw Sorted Bam file..?

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