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.
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