Relationship between Ploidy, Alleles and Genotypes

Introduction

Ploidy, alleles are independent characteristics that give rise to genotypes.

Table

Case	Alleles	Genotypes	Index	comments
ploidy \le alleles	ploidy alleles ${\begin{aligned}P(G_{i,j}|R_{k})^{(l)}={\frac {P(R_{k}|G_{i,j})P(G_{i,j})^{(l-1)}}{\sum _{(i,j)}{P(R_{k}|G_{i,j})P(G_{i,j})^{(l-1)}}}}\end{aligned}}$	18794	18849	bcftools's normalization is buggy, variants were truncated despite having differing prefix.
ploidy gt alleles	-	-	-	-
#normalized after gatk	-	0	57	57 variants from GATK's normalization were left aligned by vt. 6 were biallelic and 51 were multiallelic. Note that 2 variants were changed by GATK but were not completely normalized.
#normalized after vt	-	0	0	no variants processed by vt were further normalized.