Documentation

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.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

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).

HaplotypeResolver 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
--variant
 -V
NA Input VCF file
Optional Outputs
--out
 -o
stdout File to which variants should be written
Optional Parameters
--setKey
set Key used in the INFO key=value tag emitted describing which set the combined VCF record came from
--statusKey
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

File to which variants should be written

VariantContextWriter  stdout


--setKey / -setKey

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.

String  set


--statusKey / -statusKey

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.

String  status


--variant / -V

Input VCF file

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

R List[RodBinding[VariantContext]]


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA