I am doing exome sequencing in 700 individuals from a species with a large genome and I would like to use GATK to realign around indels. I am using a reduced reference, which is still about 3Gb. I tested out the target creator, but it is taking 5 days for 12 individuals when each is done individually and this time frame is not feasible for all 700 individuals. I tried to run more in parallel (~30 individuals), but there are RAM limitations on our 250G server. I am currently testing out the program by running all 12 test samples as input for the same run and the time estimate is very long (on the order of several hundred weeks). Based on a preliminary run I have also included a vcf file with likely indels to try and speed the process. Can you suggest another way in which I can make the time frame for all 700 individuals more reasonable? Otherwise we will not be able to use this tool.