Question about speed

[tiplud]

Hi,
I am using Pindel 0.2.5b9, and using the following command :

$pindelsoftwareDIR/pindel -f $REF -i $NAME".pindel.txt" -c $interval -o $cnvsDir/$NAME.$interval -x 8 -T 12 -L $cnvsDir/$NAME.$interval.pindel.log

Here REF is the reference genome, and NAME is the name of the sample. Each interval is one gene. With these parameters it takes around 3-4 min for each interval on a 64GB machine.

I was wondering if there was a possibility of speeding up the process ( other than reducing -x or increasing -T ). Is there something I might be missing ?

Thank you,
Debayan