Question: GATK --ploidy
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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
0
gravatar for biocyberman
4.9 years ago by
biocyberman810
Denmark
biocyberman810 wrote:

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.

ADD COMMENTlink modified 11 months ago by _r_am31k • written 4.9 years ago by biocyberman810
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