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.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

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).

VariantsToBeagleUnphased specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Inputs
--variants
 -V
NA Input VCF file
Optional Outputs
--out
 -o
stdout File to which BEAGLE unphased genotypes should be written
Optional Parameters
--bootstrap_fraction
 -bs
0.0 Proportion of records to be used in bootstrap set
--bootstrap_vcf
 -bsvcf
NA Output a VCF with the records used for bootstrapping filtered out
--missing
? String to identify missing data in beagle output

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

Proportion of records to be used in bootstrap set

double  0.0  [ [ -?  ? ] ]


--bootstrap_vcf / -bsvcf

Output a VCF with the records used for bootstrapping filtered out

VariantContextWriter


--missing / -missing

String to identify missing data in beagle output

String  ?


--out / -o

File to which BEAGLE unphased genotypes should be written

PrintStream  stdout


--variants / -V

Input VCF file

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

R RodBinding[VariantContext]


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA