BeagleOutputToVCF

Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.

Category Variant Discovery Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

This walker is intended to be run after Beagle has successfully executed. The full calling sequence for using Beagle along with the GATK is:

1. Run ProduceBeagleInputWalker.

2. Run Beagle

3. Uncompress output files

4. Run BeagleOutputToVCFWalker.

Note that this walker requires all input files produced by Beagle.

Example

     java -Xmx4000m -jar dist/GenomeAnalysisTK.jar \
      -R reffile.fasta -T BeagleOutputToVCF \
      -V input_vcf.vcf \
      -beagleR2:BEAGLE /myrun.beagle_output.r2 \
      -beaglePhased:BEAGLE /myrun.beagle_output.phased \
      -beagleProbs:BEAGLE /myrun.beagle_output.gprobs \
      -o output_vcf.vcf

Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them

Additional Information

Read filters

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

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

BeagleOutputToVCF 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
--beaglePhased	RodBinding[BeagleFeature]	NA	Beagle-produced .phased file containing phased genotypes
--beagleProbs	RodBinding[BeagleFeature]	NA	Beagle-produced .probs file containing posterior genotype probabilities
--beagleR2	RodBinding[BeagleFeature]	NA	Beagle-produced .r2 file containing R^2 values for all markers
--variant	RodBinding[VariantContext]	NA	Input VCF file
Optional
--comp	RodBinding[VariantContext]	none	Comparison VCF file
-keep_monomorphic	boolean	false	If provided, we won't filter sites that beagle tags as monomorphic. Useful for imputing a sample's genotypes from a reference panel
--nocall_threshold	double	0.0	Threshold of confidence at which a genotype won't be called
--out	VariantContextWriter	stdout	VCF File to which variants 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.

--beaglePhased / -beaglePhased ( required RodBinding[BeagleFeature] )

Beagle-produced .phased file containing phased genotypes. By default, all genotypes will be marked in the VCF as "phased", using the "|" separator after Beagle. --beaglePhased binds reference ordered data. This argument supports ROD files of the following types: BEAGLE

--beagleProbs / -beagleProbs ( required RodBinding[BeagleFeature] )

Beagle-produced .probs file containing posterior genotype probabilities. These values will populate the GL field for each sample and contain the posterior probability of each genotype given the data after phasing and imputation. --beagleProbs binds reference ordered data. This argument supports ROD files of the following types: BEAGLE

--beagleR2 / -beagleR2 ( required RodBinding[BeagleFeature] )

Beagle-produced .r2 file containing R^2 values for all markers. This required argument is used to annotate each site in the vcf INFO field with R2 annotation. Will be NaN if Beagle determined there are no variant samples. --beagleR2 binds reference ordered data. This argument supports ROD files of the following types: BEAGLE

--comp / -comp ( RodBinding[VariantContext] with default value none )

Comparison VCF file. If this argument is present, the original allele frequencies and counts from this vcf are added as annotations ACH,AFH and ANH. at each record present in this vcf --comp binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

-keep_monomorphic / --dont_mark_monomorphic_sites_as_filtered ( boolean with default value false )

If provided, we won't filter sites that beagle tags as monomorphic. Useful for imputing a sample's genotypes from a reference panel. If this argument is absent, and if Beagle determines that there is no sample in a site that has a variant genotype, the site will be marked as filtered (Default behavior). If the argument is present, the site won't be marked as filtered under this condition even if there are no variant genotypes.

--nocall_threshold / -ncthr ( double with default value 0.0 )

Threshold of confidence at which a genotype won't be called. Value between 0 and 1. If the probability of getting a genotype correctly (based on the posterior genotype probabilities and the actual genotype) is below this threshold, a genotype will be substitute by a no-call.

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

VCF File to which variants should be written.

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

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