LeftAlignVariants

Left-aligns indels from a variants file.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS

Introduction

LeftAlignVariants is a tool that takes a VCF file and left-aligns the indels inside it. The same indel can often be placed at multiple positions and still represent the same haplotype. While the standard convention with VCF is to place an indel at the left-most position this doesn't always happen, so this tool can be used to left-align them. Note that this tool cannot handle anything other than bi-allelic, simple indels. Complex events are written out unchanged.

Input

A variant set to left-align.

Output

A left-aligned VCF.

Examples

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T LeftAlignVariants \
   --variant input.vcf \
   -o output.vcf

Additional Information

Read filters

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

Window size

This tool uses a sliding window on the reference.

Window start: -200 bp before the locus
Window stop: 200 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

LeftAlignVariants 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
--out	VariantContextWriter	stdout	File to which variants should be written
--variant	RodBinding[VariantContext]	NA	Input VCF file

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.

--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 2.4-9-ge182083 built at 2013/03/19 07:40:48.