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| + | = Introduction = |
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− | Consequently, we would have the following steps.
| + | This wiki-page explains the main tools available to convert other format files to VCF format. |
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− | ===Convert GWAS Panel Files into VCF ===
| + | = Convert '''PLINK''' Files = |
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− | If pre-phased GWAS data is available in VCF format, users can skip this step. Otherwise, the following steps show how to convert other format files to VCF format.
| + | Use PLINK2 (available [https://www.cog-genomics.org/plink2 here]) as follows: |
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− | * '''PLINK:''' Use PLINK2 (available [https://www.cog-genomics.org/plink2 here]) as follows:
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| plink --bfile Gwas.Chr20.Phased.Output \ | | plink --bfile Gwas.Chr20.Phased.Output \ |
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| --out Gwas.Chr20.Phased.Output.VCF.format | | --out Gwas.Chr20.Phased.Output.VCF.format |
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− | * '''MaCH:''' Use Mach2VCF (coming soon) as follows:
| + | = Convert '''MaCH''' Files = |
| + | |
| + | Use Mach2VCF (available [ftp://share.sph.umich.edu/minimac3/Mach2VCF.v1.Source.Binary.tar.gz here]) as follows: |
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| mach2VCF --haps Gwas.Chr20.Phased.Output.hap \ | | mach2VCF --haps Gwas.Chr20.Phased.Output.hap \ |
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| --prefix Gwas.Chr20.Phased.Output.VCF.format | | --prefix Gwas.Chr20.Phased.Output.VCF.format |
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− | * '''SHAPEIT:''' Use SHAPEIT (available [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]) as follows:
| + | = Convert '''SHAPEIT''' Files = |
| + | |
| + | Use SHAPEIT (available [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]) as follows: |
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| shapeit -convert \ | | shapeit -convert \ |
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| --output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf | | --output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf |
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− | === Download Reference Panel === | + | = 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]] |
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− | Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 (available for download in [[#Reference Panels for Download |Reference Panels ]]) or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[#Reference Panels for Download |Reference Panels]].
| + | * [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''') |
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− | === Impute Samples ===
| + | * [[Minimac3 Cookbook : Pre-Phasing | Pre-Phasing ]] |
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− | The final step for imputation involves running '''Minimac3''' to perform the imputation analysis. Now that we have the pre-phased GWAS panel (in VCF format) and the appropriate reference panel (in VCF or <code>M3VCF</code> format), we can run Minimac3 as follows. In the following examples, the first one uses a VCF file for reference (that can be obtained as explained above) and the second example uses a <code>M3VCF</code> file (that might have been downloaded from the links [[#Reference Panels for Download|below]] or created on a previous run of Minimac3).
| + | * [[Minimac3 Cookbook : Converting Files to VCF| Converting Files to VCF]] |
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− | ../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.vcf \
| + | = Contact = |
− | --haps Gwas.Chr20.Phased.Output.VCF.format.vcf \
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− | --prefix Gwas.Chr20.Imputed.Output
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− | ../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.m3vcf \
| + | In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das]. |
− | --haps Gwas.Chr20.Phased.Output.VCF.format.vcf \
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− | --prefix Gwas.Chr20.Imputed.Output
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