Can GATK be used for for polyploids

hi..
I am new to this forum.. I wanted to know if i can use GATK UnifiedGenotyper for variant detection in polyploid like wheat. I am actually confused because i see it has ploidy setting but i donot find any reference for polyploids. Kindly, help me. Also plz give me the link where i can find a clear documentation about what workflow it has for variant detection.

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  • raj_123raj_123 IndiaMember
    edited December 2013

    Thanks Geraldine_VdAuwera for your answer but does that mean that i cannot go further steps of GATK workflow because as i am working on wheat RNA sequence data for which i donot have known variant data. make me correct if i am wrong GATK has the following workflow first generating mapped data i.e. BAM output file followed by variant detection using UnifiedGenotyper followed by VariantQuality Recaliberation after which we go for Annotation, the last two steps (VariantQualityRecalibration and Annotation) require known variant data which i donot have. Now can i use GATK for variant calling without quality recalibration or annotation.Kindly help me.

    Thanks in advance,

    Post edited by raj_123 on
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Raj,

    You can choose between two options; either you generate your own set of known variants, which is not easy but will give you better results, or you can skip the recalibration steps, but your results may be less reliable. It's up to you.

  • raj_123raj_123 IndiaMember

    Thank you so much for your kind reply..

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