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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.
[Please note that this tool CANNOT handle missing values in the input files and may NOT work appropriately for non-Minimac3/4 VCF files]
= 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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= Installation =
= Installation =
## EXTRACT M3VCFTOOLS AND COMPILE
## EXTRACT M3VCFTOOLS AND COMPILE
git clone https://github.com/Santy-8128/DosageConvertor
cd DosageConvertor/
cd DosageConvertor/
make
make
--format 1 (or 2,3)
--format 1 (or 2,3)
This command will create three files : <code> OutPrefix.plink.dosage.gz, OutPrefix.fam, OutPrefix.map</code>. The <code>.fam</code> and <code>.map</code> formats are described [http://zzz.bwh.harvard.edu/plink/data.shtml#map here]. The <code>--format</code> parameter can take values 1, 2 and 3. Each of these values correspond to the three different formats available for PLINK dosage files (details on PLINK dosage files are given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). Note that the generated <code>OutPrefix.map</code> does NOT contain any phenotype information (which will need to be manually edited before PLINK can perform association tests). The <code>OutPrefix.fam</code> will NOT contain sex information unless chromosome X is available. See [[#Converting Chromosome X Files | Converting Chromosome X Files]] for details.
This command will create three files : <code>OutPrefix.plink.dosage.gz</code>, <code>OutPrefix.fam</code>, and <code>OutPrefix.map</code>. The <code>.fam</code> and <code>.map</code> formats are described [http://zzz.bwh.harvard.edu/plink/data.shtml#map here]. The <code>--format</code> parameter can take values 1, 2, or 3. Each of these values correspond to the three different PLINK dosage file formats (details on PLINK dosage files are given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). Note that the generated <code>OutPrefix.map</code> does NOT contain any phenotype information (which will need to be manually edited before PLINK can perform association tests). The <code>OutPrefix.fam</code> will NOT contain sex information unless chromosome X is available. See [[#Converting Chromosome X Files | Converting Chromosome X Files]] for details.
== Convert to MaCH Files ==
== Convert to MaCH Files ==
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].
./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz
./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz
--format 1 (or 2)
--format 1 (or 2)
When <code>--type mach</code> is used, the <code>--format</code> parameter can only take values 1 and 2.
When <code>--type mach</code> is used, the <code>--format</code> parameter can only take values 1 or 2.
*If the value is 1, the code generates <code>OutPrefix.mach.dose.gz</code> and <code>OutPrefix.info</code>, where <code>OutPrefix.mach.dose.gz</code> contains the expected alternate allele count (one value per sample per marker).
*If the value is 1, the code generates <code>OutPrefix.mach.dose.gz</code> and <code>OutPrefix.info</code>, where <code>OutPrefix.mach.dose.gz</code> contains the expected alternate allele count (one value per sample per marker).
== Converting Chromosome X Files ==
== Converting Chromosome X Files ==
For a minimac3/4 output file containing the pseudo-autosomal region (PAR) on chromosome X, no extra parameter is necessary. For files containing the non-PAR region, please ensure the following:
For conversion of X chromosome files from minimac3/4, please ensure the following:
* If your input VCF dosage file has '''males as diploids''', then just add handle <code>--allDiploid</code>. This will NOT generate sex information in the output PLINK <code>.fam</code> file.
* If your input VCF dosage file has '''males as diploids''', then just add handle <code>--allDiploid</code>. This will NOT generate sex information in the output PLINK <code>.fam</code> file.
** If you still need the sex column in <code>.fam</code> file to be correctly updated, then supply a sex file using <code>--sexFile SomeFile</code> where <code>SomeFile</code> has two columns: the first column has the sample names as found in the VCF file, and the second columns has M (for males) or F (for females).
** If you still need the sex column in <code>.fam</code> file to be correctly updated, then supply a sex file using <code>--sexFile SomeFile</code> where <code>SomeFile</code> has two columns:
* If your input VCF dosage file has '''males as haploids''' and '''also has GT information''', the tool with automatically determine the sex of the samples and report them in the output <code>.fam</code> file. No extra parameters are required.
*** the first column has the sample names as found in the VCF file
** If GT tags are NOT available, you would need to supply the sex file as described above. Otherwise it will throw an error.
*** the second columns has M (for males) or F (for females).
** '''NOTE''': If your VCF file has males as haploids, do NOT use <code>--allDiploid</code> as the code would NOT throw any error, but the output results would be erroneous.
* If your input VCF dosage file has '''males as haploids''' and '''also has GT information''', the tool with automatically determine the sex of the samples from their ploidy and report them in the output <code>.fam</code> file. No extra parameters are required.
** If '''GT''' tags are NOT available, you would need to supply the <code>--sexFile</code> as described above. Otherwise it will throw an error.
** '''NOTE''': If your VCF file has males as haploids, do NOT use <code>--allDiploid</code> as the output results would be erroneous (although the code would NOT throw any error)
= Command Line Options =
= Command Line Options =
The command options for DosageConvertor are explained below.
The command options for DosageConvertor are explained below.
{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
{| class="wikitable" style="text-align:left" border="1" cellpadding="2"
|- bgcolor="white"
|- bgcolor="white"
! Option
! Option
| <code>--prefix</code>
| <code>--prefix</code>
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sets the prefix for output files (default value: <code>Converted.Dosage</code>)
sets the prefix for output files (default: <code>Converted.Dosage</code>)
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| <code>--type</code>
| <code>--type</code>
| <code>--tag</code>
| <code>--tag</code>
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indicates whether to import imputed values from dosages (<code>DS</code>: default), genotype probabilities (<code>GP</code>), or hard genotype calls (<code>GT</code>) from the input VCF file
indicates the FORMAT tag of the VCF file from which to import the imputed dosages:
*<code>DS</code>: imputed values from dosages (default)
*<code>GP</code>: genotype probabilities
*<code>GT</code>: hard genotype calls
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|-
| <code>--format</code>
| <code>--format</code>
sets the format of the converted output file:
sets the format of the converted output file:
*If <code>--type plink</code> is used, <code>--format</code> can take values 1, 2, or 3. Each of these values correspond to the three different formats available for PLINK dosage files (details given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here])
*If <code>--type plink</code> is used, <code>--format</code> can take values 1, 2, or 3.
*If <code>--type mach</code> is used, <code>--format</code> can take values 1 or 2. Details are given in [[#Convert to MaCH Files| Convert to MaCH Files]]
Each of these values correspond to the three different formats available for PLINK dosage files (details given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here])
*If <code>--type mach</code> is used, <code>--format</code> can take values 1 or 2.
Details are given in [[#Convert to MaCH Files| Convert to MaCH Files]]
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| <code>--buffer</code>
| <code>--buffer</code>
| <code>--allDiploid</code>
| <code>--allDiploid</code>
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indicates whether to assume all samples are diploid (necessary for chromosome X). If this option is active, the output PLINK <code>.fam</code> will NOT contain any sex information
indicates whether to assume all samples are diploid (necessary for chromosome X).
If this option is active, the output PLINK <code>.fam</code> will NOT contain any sex information
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| <code>--sexFile</code>
| <code>--sexFile</code>
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indicates a file containing sample sex information, which requires two columns: the first column contains the sample names as found in the VCF file, and the second columns contains either M (for males) or F (for females)
indicates a file containing sample sex information, which requires two columns:
*the first column contains the sample names as found in the VCF file
*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. Since PLINK does not allow variant IDs longer than 16,000 characters, this option can be used if variant names are too long
indicates whether to trim variants IDs to 100 characters
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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