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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,