Changes

= Info File Descriptors =

= Info File Descriptors =

The available column descriptors for typical Miniamc3 output are as follows:

The available column descriptors for typical Miniamc3 output are as follows.

==='''SNP'''===

==='''SNP'''===

This is the estimated value of the squared correlation between imputed genotypes and true, unobserved genotypes. Since true genotypes are not available, this calculation is based on the idea that poorly imputed genotype counts will shrink towards their expectations based on population allele frequencies alone; specifically <math>2p</math> where <math>p</math> is the frequency of the allele being imputed.

This is the estimated value of the squared correlation between imputed genotypes and true, unobserved genotypes. Since true genotypes are not available, this calculation is based on the idea that poorly imputed genotype counts will shrink towards their expectations based on population allele frequencies alone; specifically <math>2p</math> where <math>p</math> is the frequency of the allele being imputed.

Currently, Minimac3 uses the following definition:

Currently, Minimac3 uses the following definition (where <math>\hat{p}</math> is the alternate allele frequency and <math>D_i</math> is the imputed alternate allele probability at the <math>i^{th}</math> haplotype and <math>n</math> is the number of GWAS samples) :

:<math>\hat{r}^2 = {{Var(\mbox{Estimated Counts})}\over{\hat{p}(1-\hat{p})}}</math>

:<math>\hat{r}^2 = {{ {{1}\over{2n}} \times \sum_{i=1}^{2n} {(D_i - \hat{p})^2} }\over{\hat{p}(1-\hat{p})}}</math>

==='''Genotyped'''===

==='''Genotyped'''===

==='''Dose1'''===

==='''Dose1'''===

==='''Dose2'''===

==='''Dose2'''===