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, 02:02, 30 January 2015
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| * '''Pre-phase PAR data and female non-PAR data:''' Out of the three available data, only the PAR data and female non-PAR data have two haplotypes and thus need to be phased, while the male non-PAR data has haploids and need not be phased. See our wiki page on [[Minimac3 Cookbook : Pre-Phasing| Pre-Phasing]] and [[Minimac3 Cookbook : Converting Files to VCF| Converting to VCF]] for further details on pre-phasing and converting files back to VCF format. | | * '''Pre-phase PAR data and female non-PAR data:''' Out of the three available data, only the PAR data and female non-PAR data have two haplotypes and thus need to be phased, while the male non-PAR data has haploids and need not be phased. See our wiki page on [[Minimac3 Cookbook : Pre-Phasing| Pre-Phasing]] and [[Minimac3 Cookbook : Converting Files to VCF| Converting to VCF]] for further details on pre-phasing and converting files back to VCF format. |
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− | * '''Impute Data:''' The following example illustrates how to impute into the pahsed PAR data (both males and females together), phased female non-PAR data and haploid male non-PAR data as follows: | + | * '''Impute Data:''' The following example illustrates how to impute into the phased PAR data (both males and females together), phased female non-PAR data and haploid male non-PAR data (same as obtained after splitting the non-PAR by sex) as follows: |
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− | # Male Samples (Non-PAR) | + | # Phased All Samples (PAR) |
− | ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \ | + | ../bin/Minimac3 --refHaps refPanelChrX.Auto.vcf \ |
− | --haps Phased.Male.Non.PAR.gwas.data.vcf \ | + | --haps Phased.PAR.gwas.data.vcf \ |
− | --prefix testRun.males.Non.PAR | + | --prefix testRun.All.PAR |
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− | # Female Samples (Non-PAR) | + | # Phased Female Samples (Non-PAR) |
| ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \ | | ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \ |
| --haps Phased.Female.Non.PAR.gwas.data.vcf \ | | --haps Phased.Female.Non.PAR.gwas.data.vcf \ |
| --prefix testRun.females.Non.PAR | | --prefix testRun.females.Non.PAR |
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− | # All Samples (PAR) | + | # Haploid Male Samples (Non-PAR) |
| ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \ | | ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \ |
− | --haps PAR.gwas.data.recode.vcf \ | + | --haps Male.Non.PAR.gwas.data.recode.vcf \ |
− | --prefix testRun.All.PAR | + | --prefix testRun.males.Non.PAR |
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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. |