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Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

GATK on alternate life cycle organimsm - ploidy

mstagliamontemstagliamonte USAMember Posts: 12

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,

Max

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  • mstagliamontemstagliamonte USAMember Posts: 12

    Thank you :)

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

    Regards,
    Max

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