GATK Indel realignment taking too long

[abolia]

Hi,

We have been testing Whisper on our large targeted capture data. The results look pretty encouraging as whisper takes only half the time taken by BWA-Mem. However, when you use GATK Indel realigner to realign the reads from Whisper, it ends up taking 5 times the total time required by IndelRealigner to realign BWA-Mem reads. I was wondering if you have any insights on what could be happening here and if there is a way to improve the overall efficiency.

Thanks,
Ashini