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Revision as of 23:33, 29 January 2015
, 23:33, 29 January 2015→Introduction
= Introduction =
= Introduction =
[http://genome.sph.umich.edu/wiki/Minimac3 '''Minimac3 '''] is a lower memory and more computationally efficient implementation of [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]. It is an algorithm for genotypic imputation that works on phased genotypes and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
This wiki page is designed to give users a '''detailed step-by-step description on running typical GWAS imputation experiments'''.
= Chromosome X Imputation =
Chromosome X has a pseudo-autosomal region (PAR) which can be imputed for males and females together. Imputing the PAR on chromosome X is same as usual imputation, since both males and females are diploids at these sites. However, the non pseudo-autosomal region needs to be imputed for males and females separately, as males are haploids while females are diploids. Of course, the PAR and non-PAR regions need to be imputed separately. This wiki page gives further details on imputing chromosome X.
Chromosome X has a pseudo-autosomal region (PAR) which can be imputed for males and females together. Imputing the PAR on chromosome X is same as usual imputation, since both males and females are diploids at these sites. However, the non pseudo-autosomal region needs to be imputed for males and females separately, as males are haploids while females are diploids. Of course, the PAR and non-PAR regions need to be imputed separately. This wiki page gives further details on imputing chromosome X.
NOTE: For imputing non-PAR of chromosome X, user must analyze male and female samples separately, otherwise program would crash. User should also ensure that the reference panel consists of only PAR or non-PAR region of chromosome X, otherwise program would crash.
NOTE: For imputing non-PAR of chromosome X, user must analyze male and female samples separately, otherwise program would crash. User should also ensure that the reference panel consists of only PAR or non-PAR region of chromosome X, otherwise program would crash.
= Download =
'''Minimac3 ''' is currently available as a pre-release. The source files (and binary executable) are available for download in [[Minimac3#Download | Source Files]] and commonly used reference panels in VCF and <font face=Courier>M3VCF</font> formats are available for download in [[Minimac3#Reference Panels for Download | Reference Panels]].
= Useful Wiki Pages =
There are a few pages in this Wiki that may be useful to for '''Minimac3''' users. Here are links to a few:
* [[Minimac3| Minimac3 Overview Page]]
* [[Minimac3 Usage | Minimac3 Usage and Documentation]]
* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')
* [[Minimac3 Cookbook : Chromosome X Imputation | Chromosome X Imputation ]]
* [[Minimac3 Cookbook : Pre-Phasing | Pre-Phasing ]]
* [[Minimac3 Examples| Minimac3 Examples]]
* [[M3VCF Files| M3VCF Files]]
= Contact =
In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].
