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Relationship between Ploidy, Alleles and Genotypes (view source)

Revision as of 10:36, 31 January 2015

317 bytes removed ,  10:36, 31 January 2015
→‎Simple cases
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{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
−
! scope="col"| Case
+
! scope="col"| Ploidy
 
! scope="col"| Alleles
 
! scope="col"| Alleles
 
! scope="col"| Genotypes
 
! scope="col"| Genotypes
 
! scope="col"| Index
 
! scope="col"| Index
−
! scope="col"| comments
   
|-
 
|-
−
| ploidy \le  alleles
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| 1
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| ploidy  alleles
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| A
−
<math>
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| A
−
  \begin{align}
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| Simple haploid case
−
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}
  −
</math>
  −
| 18794
  −
| 18849
  −
| bcftools's normalization is buggy, variants were truncated despite having differing prefix.
   
|-
 
|-
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| ploidy gt alleles
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| 2
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| -
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| A
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| -
+
|  
−
| -
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| Diploid Case
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| -
   
|-
 
|-
 
| #normalized after gatk
 
| #normalized after gatk
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| -
   
| 0
 
| 0
 
| 57
 
| 57
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| #normalized after vt
 
| #normalized after vt
 
| -
 
| -
−
| 0
   
| 0
 
| 0
 
| no variants processed by vt were further normalized.
 
| no variants processed by vt were further normalized.
 
|}
 
|}
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