HaplotypeResolver

Haplotype-based resolution of variants in 2 different eval files.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

HaplotypeResolver is a tool that takes 2 VCF files and constructs haplotypes based on the variants inside them. From that, it can resolve potential differences in variant calls that are inherently the same (or similar) variants. Records are annotated with the set and status attributes.

Input

2 variant files to resolve.

Output

A single consensus VCF.

Examples

 java -Xmx1g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T HaplotypeResolver \
   -V:v1 input1.vcf \
   -V:v2 input2.vcf \
   -o output.vcf

Additional Information

Read filters

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

Window size

This tool uses a sliding window on the reference.

Window start: -1,100 bp before the locus
Window stop: 1,100 bp after the locus

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

HaplotypeResolver 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
--variant	List[RodBinding[VariantContext]]	NA	Input VCF file
Optional
--out	VariantContextWriter	stdout	File to which variants should be written
--setKey	String	set	Key used in the INFO key=value tag emitted describing which set the combined VCF record came from
--statusKey	String	status	Key used in the INFO key=value tag emitted describing the extent to which records match

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.

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

File to which variants should be written.

--setKey / -setKey ( String with default value set )

Key used in the INFO key=value tag emitted describing which set the combined VCF record came from. Set to 'null' if you don't want the set field emitted.

--statusKey / -statusKey ( String with default value status )

Key used in the INFO key=value tag emitted describing the extent to which records match. Set to 'null' if you don't want the status field emitted.

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

Input VCF 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.