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Revision as of 09:51, 31 January 2015
, 09:51, 31 January 2015Created page with "= Introduction = Ploidy, alleles are independent characteristics that give rise to genotypes. = Table = {| class="wikitable" |- ! scope="col"| Case ! scope="col"| Alleles ..."
= Introduction =
Ploidy, alleles are independent characteristics that give rise to genotypes.
= Table =
{| class="wikitable"
|-
! scope="col"| Case
! scope="col"| Alleles
! scope="col"| Genotypes
! scope="col"| Index
! scope="col"| comments
|-
| ploidy \le alleles
| ploidy alleles
<math>
\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}
</math>
| 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.
|}
Ploidy, alleles are independent characteristics that give rise to genotypes.
= Table =
{| class="wikitable"
|-
! scope="col"| Case
! scope="col"| Alleles
! scope="col"| Genotypes
! scope="col"| Index
! scope="col"| comments
|-
| ploidy \le alleles
| ploidy alleles
<math>
\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}
</math>
| 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.
|}
