- Download/Re-Clone Release Version 1.0.4 (Updated July 2017) !
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.
VERSION: 1.0.4 (Updated 7.12.2017) !
[NOTE: Cloning from GitHub is recommened so that updates can be easily pulled back]
| Binary Executable †
† 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 github repository. Else contact the author Sayantan Das.
Users should follow the following steps to compile DosageConvertor (if they downloaded the source files).
## EXTRACT M3VCFTOOLS AND COMPILE wget ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.3.tar.gz tar -xzvf DosageConvertor.v1.0.3.tar.gz cd DosageConvertor/ make
Convert to PLINK Files
./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz --info TestDataImputedVCF.info (optional) --prefix OutPrefix --type plink (default) --format 1 (or 2,3)
This command will create three files :
OutPrefix.plink.dosage.gz, OutPrefix.fam, OutPrefix.map. The
.map formats are described here. The
--format 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 here). Note that the generated
OutPrefix.map does NOT contain any phenotype information (which will need to be manually edited before PLINK can perform association tests). The
OutPrefix.fam will NOT contain sex information unless chromosome X is available. See Converting Chromosome X Files for details.
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). The generated dosage files can be tested for association using mach2dat.
./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz --info TestDataImputedVCF.info (optional) --prefix OutPrefix --type mach --format 1 (or 2)
--type mach is used, the
--format parameter can only take values 1 and 2.
- If the value is 1, the code generates
OutPrefix.mach.dose.gzcontains the expected alternate allele count (one value per sample per marker).
- If the value is 2, it generates
OutPrefix.mach.gprob.gzcontains the genotype likelihoods for reference homozygote and heterozygote (two values per sample per marker).
Note that inputting the info file using
--info is optional. However, if this info file is NOT provided, the output
OutPrefix.info file will have some empty columns. Thus, if available, the generated info file should be provided along with the VCF file as input.
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:
- If your input VCF dosage file has males as diploids, then just add handle
--allDiploid. This will NOT generate sex information in the output PLINK
- If you still need the sex column in
.famfile to be correctly updated, then supply a sex file using
SomeFilehas 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
- 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
.famfile. No extra parameters are required.
- If GT tags are NOT available, you would need to supply the sex file as described above. Otherwise it will throw an error.
- NOTE: If your VCF file has males as haploids, do NOT use
--allDiploidas the code would NOT throw any error, but the output results would be erroneous.
Command Line Options
The command options for DosageConvertor are explained below.
--vcfDoseis a mandatory parameter indicating the minimac3/4 VCF dosage file to be converted
--infois the info file generated by minimac3/4 at the same time as the VCF dosage file. This parameter is optional, but if NO info file is provided, the output MaCH info file will have missing columns
--prefixsets the prefix for output files (default value:
--typesets the output file format (available options:
--tagindicates whether to import imputed values from dosages (
DS: default), genotype probabilities (
GP), or hard genotype calls (
GT) from the input VCF file
--formatsets the format of the converted output file.
--buffersets the number of markers to import at a time (MaCH format only) (default value
--idDelimiterdenotes the delimiter character used to split VCF Sample ID into FID and IID for PLINK format
--allDiploiddenotes whether to assume all samples are diploid (necessary for chromosome X). If this handle is on, the output PLINK
.famwill NOT contain any sex information.
--sexFiledenotes the sex file which should have 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).
--TrimAllelesdenotes whether to trim length of alleles and variants IDs since PLINK does NOT allow really long character sequences.
In case of any queries and bugs please contact Sayantan Das.