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| = Introduction = | | = Introduction = |
| DosageConvertor is a C++ tool to convert dosage files (in VCF format) from [[Minimac4| Minimac3/4]] to other formats such as MaCH or PLINK. | | DosageConvertor is a C++ tool to convert dosage files (in VCF format) from [[Minimac4| Minimac3/4]] to other formats such as MaCH or PLINK. |
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| + | [Please note that this tool CANNOT handle missing values in the input files and may NOT work appropriately for non-Minimac3/4 VCF files] |
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| = Download = | | = Download = |
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| [https://github.com/Santy-8128/DosageConvertor DosageConvertor - Github] | | [https://github.com/Santy-8128/DosageConvertor DosageConvertor - Github] |
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− | | Source Files
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− | [ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.3.tar.gz UNIX Users ]
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− | | Binary Executable <sup>†</sup>
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− | (Ubuntu 4.8.4)
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− | [ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertorExecutable.tar.gz UNIX Users ]
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| |} | | |} |
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− | '''<sup>†</sup>''' Binary executables are NOT guaranteed to run on every LINUX machine. Please compile from source files if you have trouble with the executable, or clone from the [https://github.com/Santy-8128/DosageConvertor github repository]. Else contact the author [mailto:sayantan@umich.edu Sayantan Das].
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| = Installation = | | = Installation = |
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| ## EXTRACT M3VCFTOOLS AND COMPILE | | ## EXTRACT M3VCFTOOLS AND COMPILE |
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− | wget ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.3.tar.gz | + | git clone https://github.com/Santy-8128/DosageConvertor |
− | tar -xzvf DosageConvertor.v1.0.3.tar.gz
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| cd DosageConvertor/ | | cd DosageConvertor/ |
| make | | make |
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| == Convert to MaCH Files == | | == Convert to MaCH Files == |
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− | The following command will convert an input VCF dosage file to a MaCH/minimac dosage file (the format for previous versions of [[Minimac | minimac]]). The generated dosage files can be tested for association using [http://genome.sph.umich.edu/wiki/Mach2dat:_Association_with_MACH_output mach2dat]. | + | The following command will convert an input VCF dosage file to a MaCH/minimac dosage file (the format for previous versions of [[Minimac | minimac]]). The generated dosage files can be tested for association using tools like [http://genome.sph.umich.edu/wiki/Mach2dat:_Association_with_MACH_output mach2dat] or [http://www.genabel.org/packages/ProbABEL ProbABEL]. |
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| ./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz | | ./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz |
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| | <code>--tag</code> | | | <code>--tag</code> |
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− | indicates the FORMAT tag of the VCF from which to import the imputed dosages: | + | indicates the FORMAT tag of the VCF file from which to import the imputed dosages: |
| *<code>DS</code>: imputed values from dosages (default) | | *<code>DS</code>: imputed values from dosages (default) |
| *<code>GP</code>: genotype probabilities | | *<code>GP</code>: genotype probabilities |
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| *the second columns contains either M (for males) or F (for females) | | *the second columns contains either M (for males) or F (for females) |
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− | | <code>--TrimAlleles</code> | + | | <code>--trimNames</code> |
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− | indicates whether to trim alleles and variants IDs to 100 characters | + | indicates whether to trim variants IDs to 100 characters |
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| Since PLINK does not allow variant IDs longer than 16,000 characters, this option can be used if variant names are too long. | | Since PLINK does not allow variant IDs longer than 16,000 characters, this option can be used if variant names are too long. |
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| + | | <code>--trimLength</code> |
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| + | number (<16000) indicating the length to which to trim variants IDs to (default value : 100) |
| |} | | |} |
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