Relationship between Ploidy, Alleles and Genotypes
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Introduction
Ploidy, alleles are independent characteristics that give rise to genotypes.
Table
Case | Alleles | Genotypes | Index | comments |
---|---|---|---|---|
ploidy \le alleles | ploidy alleles
|
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. |