LeftAlignAndTrimVariants

Left-aligns indels from a variants file.

Overview

LeftAlignAndTrimVariants 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. Optionally, the tool will also trim common bases from indels, leaving them with a minimum representation.

Input

A variant set to left-align and trim.

Output

A left-aligned VCF.

Examples

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


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

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: -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).

LeftAlignAndTrimVariants 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
NA File to which variants should be written
Optional Flags
--splitMultiallelics
-split
NA Split multiallelic records and left-align individual alleles
--trimAlleles
-trim
NA Trim alleles to remove bases common to all of them

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

--splitMultiallelics / -split

Split multiallelic records and left-align individual alleles
If this argument is set, split multiallelic records and left-align individual alleles. If this argument is not set, multiallelic records are not attempted to left-align and will be copied as is.

boolean

--trimAlleles / -trim

Trim alleles to remove bases common to all of them
If this argument is set, bases common to all alleles will be removed, leaving only their minimal representation.

boolean

--variant / -V

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

R RodBinding[VariantContext]