User contributions
9 July 2013
Variant Normalization
How to observe that a variant is not left aligned?
+34
Variant Normalization
Normalization
-2
Variant Normalization
no edit summary
+292
Variant Normalization
no edit summary
+4
Left alignment
Redirected page to Variant Normalization
Left alignment
Redirected page to Variant normalization
Variant Normalization
Created page with '= Introduction = Variant representation in Variant Call Format is non unique. We describe a variant normalization here that is parsimonious and left aligned. = Normalization =…'
File:Variant normalization algorithm.png
no edit summary
File:Left alignment.png
no edit summary
File:Left alignment.pdf
no edit summary
4 June 2013
HWEP
Redirected page to Genotype Likelihood based Hardy-Weinberg Test
-1,681
AF
Redirected page to Genotype Likelihood based Allele Frequency
-2,329
Genotype Likelihood based Inbreeding Coefficient
Introduction
-5
Genotype Likelihood based Inbreeding Coefficient
Introduction
-2
Genotype Likelihood based Hardy-Weinberg Test
Created page with '=== Introduction === This page details a Hardy-Weinberg Equilibrium test based on genotype likelihoods in NGS data. === Formulation === Hardy Weinberg equilibrium is expected …'
Genotype Likelihood based Allele Frequency
Introduction
-3
Genotype Likelihood based Inbreeding Coefficient
Created page with '=== Introduction === Inbreeding Coefficients are an important statistic in the study of genetic variants. This page details EM algorithms to estimate inbreeding coefficients fro…'
FIC
Redirected page to Genotype Likelihood based Inbreeding Coefficient
-35
FIC
Redirected page to Https://statgen.sph.umich.edu/wiki/Genotype Likelihood based Inbreeding Coefficient
-1,901
Genotype Likelihood based Allele Frequency
Created page with '=== Introduction === Allele frequencies are an important statistic in the study of genetic variants. This page details EM algorithms to estimate allele frequencies from genoty…'
18 May 2013
11 April 2013
FIC
Formulation
+29
FIC
Formulation
+212
FIC
no edit summary
+22
FIC
no edit summary
-1
HWEP
Derivation
-27
AF
Derivation by
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AF
Derivation by
+104
AF
Estimation of Genotype Frequencies without assuming HWE
+11
AF
Estimation of Genotype Frequencies without assuming HWE
+66
FIC
no edit summary
+14
HWEP
Maintained by
-22
HWEP
Maintained by
+54
AF
no edit summary
+31
FIC
no edit summary
-1
AF
Estimation of Genotype Frequencies without assuming HWE
+20
HWEP
no edit summary
+21
HWEP
no edit summary
-8
HWEP
Created page with 'Hardy Weinberg equilibrium is expected in a panmictic population. The following formulation is a likelihood ratio test statistic that incorporates the genotype uncertainty via g…'
FIC
no edit summary
+110
AF
Created page with '=== Estimation of Genotype Frequencies without assuming HWE === We propose an EM algorithm to estimate the genotype frequencies without assuming HWE. The posterior probability …'
FIC
Created page with 'Many data sets consist of individuals from different populations, in the cases of structured populations, this usually result in an increased number of homozygotes. The inbreedi…'
