When I use GATK to conduct SNP detection, I have seen that the default value of 'GATK -ploidy' is 2. I am working on rice. Then if my single data set is from pooled DNA extracted from 8 rice plants, I set the -ploidy as the default. Then if I get 8 different data sets, I set the -ploidy to be 2*8. Am I right?
Yes. That's right. See more here to get the whole picture: http://gatkforums.broadinstitute.org/gatk/discussion/1214/can-i-use-gatk-on-non-diploid-organisms
It has nothing to do with the default ploidy value though. You make 2*8 because rice happens to be diploidy, and you have 8 kinds of rice.