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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

GATK on alternate life cycle organimsm - ploidy

Dear Team,

Thank you for GATK, which I am learning to use and already considering a great tool. I am trying to analyze a whole genome shotgun dataset from Plasmodium species and trying to decide what ploidy I should use.
My dataset comes from a human blood sample. Plasmodia have a brief sexual stage in the mosquito (diploid phase), but then reproduce asexually in the blood of the mammal host (haploid phase). Of course, if the diploid organisms was heterozygous for a certain trait, we are going to have a heterozygous population in the mammalian host. Also, multiclonal infections are possible, it means that more than 2 alleles for the same trait may be present in the blood.

I am sorry for the novice question, what would you suggest me regarding the ploidy parameter?

Thanks for your time and attention,
Kind Regards,



Best Answer


  • Thank you :)

    I'll keep looking around and see what I find.


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