VariantsToBeagleUnphased

Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample in input variant file.

Category Variant Discovery Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

Will additionally hold back a fraction of the sites for evaluation, marking the genotypes at that sites as missing, and writing the truth of these sites to a second VCF file

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by VariantsToBeagleUnphased.

Command-line Arguments

Inherited arguments

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).

CommandLineGATK

VariantsToBeagleUnphased specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Required
--variants	RodBinding[VariantContext]	NA	Input VCF file
Optional
--bootstrap_fraction	double	0.0	Proportion of records to be used in bootstrap set
--bootstrap_vcf	VariantContextWriter	NA	Output a VCF with the records used for bootstrapping filtered out
--missing	String	?	String to identify missing data in beagle output
--out	PrintStream	stdout	File to which BEAGLE unphased genotypes should be written

Argument details

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.

--bootstrap_fraction / -bs ( double with default value 0.0 )

Proportion of records to be used in bootstrap set.

--bootstrap_vcf / -bsvcf ( VariantContextWriter )

Output a VCF with the records used for bootstrapping filtered out.

--missing / -missing ( String with default value ? )

String to identify missing data in beagle output.

--out / -o ( PrintStream with default value stdout )

File to which BEAGLE unphased genotypes should be written.

--variants / -V ( required RodBinding[VariantContext] )

Input VCF file. --variants binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.