Difference between revisions of "Minimac3 Cookbook : Chromosome X Imputation"
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= Introduction = | = Introduction = | ||
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| + | [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. | ||
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| + | 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. | ||
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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]. | ||
Revision as of 23:33, 29 January 2015
Introduction
Minimac3 is a lower memory and more computationally efficient implementation of 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.
The following example illustrates imputation on the non-PAR of chromosome X for males and females separately (files available in Minimac3/test/ directory)
Male Samples (Non-PAR)
../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.males.vcf --prefix testRun
Female Samples (Non-PAR)
../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.females.vcf --prefix testRun
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 Source Files and commonly used reference panels in VCF and M3VCF formats are available for download in 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 Imputation Cookbook (Recommended for New Users!!)
Contact
In case of any queries and bugs please contact Sayantan Das.
