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Relationship between Ploidy, Alleles and Genotypes

Revision as of 09:51, 31 January 2015 by Atks (talk | contribs) (Created page with "= Introduction = Ploidy, alleles are independent characteristics that give rise to genotypes. = Table = {| class="wikitable" |- ! scope="col"| Case ! scope="col"| Alleles ...")
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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


  \begin{align}
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{align}

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.