Question: GATK --ploidy
gravatar for zhengyunchaosky
4.9 years ago by
Technical University of Munich
zhengyunchaosky20 wrote:

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? 

snp • 1.7k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by zhengyunchaosky20

Thank you for your clear answer!!

ADD REPLYlink written 4.9 years ago by zhengyunchaosky20
gravatar for biocyberman
4.9 years ago by
biocyberman810 wrote:

Yes. That's right. See more here to get the whole picture:

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.

ADD COMMENTlink modified 11 months ago by _r_am31k • written 4.9 years ago by biocyberman810
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1827 users visited in the last hour