GATK --ploidy

Question

[zhengyunchaosky]

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?

Answer 1

[biocyberman]

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.

[zhengyunchaosky]

Thank you for your clear answer!!