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what is mathematical detail of ploidy run in GATK
I am working on reference genome whose ploidy level is 4 (tetra-ploidy species) . I want to know the basic principle behind usage of -ploidy in GATK while analyzing variants in any mapping file. I explored all the three citation available till date (McKenna et al. 2010 ,DePristo et al. 2011, Auwera et al. 2013) of GATK. These papers helped me in protocol run . All i got to know "GATK based on the Bayesian genotyper" , performs mathematical calculation for prior probability based on the Bayesian formulation as given by Shoemaker et al. 1999.
Still question of ploidy that how exactly it interfer the SNP call is not clear to me .
What is the exact mathematical formulation used while performing the ploidy caluclation as per user request. Please make it clear to me by mean of some example.
I will be grateful to you .