Converts a VCF file to a binary plink Ped file (.bed/.bim/.fam)
These Read Filters are automatically applied to the data by the Engine before processing by VariantsToBinaryPed.
This tool applies the following downsampling settings by default.
This tool uses a sliding window on the reference.
The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--metaData||File||NA||Sample metadata file. You may specify a .fam file (in which case it will be copied to the file you provide as fam output).|
|--variant||RodBinding[VariantContext]||NA||Input VCF file|
|--bed||PrintStream||NA||output ped file|
|--bim||PrintStream||NA||output map file|
|--fam||PrintStream||NA||output fam file|
|--minGenotypeQuality||int||0||If genotype quality is lower than this value, output NO_CALL|
|--outputMode||OutputMode||INDIVIDUAL_MAJOR||The output file mode (SNP major or individual major)|
|--checkAlternateAlleles||boolean||false||Checks that alternate alleles actually appear in samples, erroring out if they do not|
|--majorAlleleFirst||boolean||false||Sets the major allele to be 'reference' for the bim file, rather than the ref allele|
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
output ped file.
output map file.
Checks that alternate alleles actually appear in samples, erroring out if they do not.
output fam file.
Sets the major allele to be 'reference' for the bim file, rather than the ref allele.
Sample metadata file. You may specify a .fam file (in which case it will be copied to the file you provide as fam output).. The metaData file can take two formats, the first of which is the first 6 lines of the standard ped file. This is what Plink describes as a fam file. An example fam file is (note that there is no header):
CEUTrio NA12878 NA12891 NA12892 2 -9
CEUTrio NA12891 UNKN1 UNKN2 2 -9
CEUTrio NA12892 UNKN3 UNKN4 1 -9
where the entries are (FamilyID IndividualID DadID MomID Phenotype Sex)
An alternate format is a two-column key-value file
wherein unknown parents needn't be specified. The columns are the individual ID, and a list of key-value pairs.
Regardless of which file is specified, the walker will output a .fam file alongside the bed file. If the command line has "-md [name].fam", the fam file will be subset and reordered to match the sample content and ordering of the VCF. However, if a metadata file of the alternate format is passed by "-md [name].txt", the walker will construct a formatted .fam file from the data.
If genotype quality is lower than this value, output NO_CALL.
The output file mode (SNP major or individual major).
The --outputMode argument is an enumerated type (OutputMode), which can have one of the following values:
Input VCF file. Variants from this VCF file are used by this tool as input. The file must at least contain the standard VCF header lines, but can be empty (i.e., no variants are contained in the file). --variant binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3
GATK version 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.