LeftAlignAndTrimVariants

Left-align indels in a variant callset

Category Variant Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

LeftAlignAndTrimVariants is a tool that takes a VCF file, left-aligns the indels and trims common bases from indels, leaving them with a minimum representation. 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 isn't always done, so this tool can be used to left-align them. This tool optionally splits multiallelic sites into biallelics and left-aligns individual alleles. Optionally, the tool will not trim common bases from indels.

Input

A variant call set to left-align and trim.

Output

A left-aligned VCF.

Usage examples

Left align and trim alleles

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

Left align and don't trim alleles

 java -jar GenomeAnalysisTK.jar \
   -T LeftAlignAndTrimVariants \
   -R reference.fasta \
   --variant input.vcf \
   -o output.vcf \
   --dontTrimAlleles
 

Left align and trim alleles, process alleles <= 208 bases

 java -jar GenomeAnalysisTK.jar \
   -T LeftAlignAndTrimVariants \
   -R reference.fasta \
   --variant input.vcf \
   -o output.vcf \
   --reference_window_stop 208
 

Split multiallics into biallelics, left align and trim alleles

 java -jar GenomeAnalysisTK.jar \
   -T LeftAlignAndTrimVariants \
   -R reference.fasta \
   --variant input.vcf \
   -o output.vcf \
   --splitMultiallelics
 

Split multiallelics into biallics, left align but don't trim alleles, and store the original AC, AF, and AN values

 java -jar GenomeAnalysisTK.jar \
   -T LeftAlignAndTrimVariants \
   -R reference.fasta \
   --variant input.vcf \
   -o output.vcf \
   --splitMultiallelics \
   --dontTrimAlleles
   --keepOriginalAC
 

Additional Information

Read filters

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

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

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

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
stdout File to which variants should be written
Optional Flags
--dontTrimAlleles
 -notrim
false Do not Trim alleles to remove bases common to all of them
--keepOriginalAC
false Store the original AC, AF, and AN values after subsetting
--splitMultiallelics
 -split
false Split multiallelic records and left-align individual alleles

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.


--dontTrimAlleles / -notrim

Do not Trim alleles to remove bases common to all of them
If this argument is set, bases common to all alleles will not be removed and will not leave their minimal representation.

boolean  false


--keepOriginalAC / -keepOriginalAC

Store the original AC, AF, and AN values after subsetting
When subsetting a callset, this tool recalculates the AC, AF, and AN values corresponding to the contents of the subset. If this flag is enabled, the original values of those annotations will be stored in new annotations called AC_Orig, AF_Orig, and AN_Orig.

boolean  false


--out / -o

File to which variants should be written

VariantContextWriter  stdout


--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  false


--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).

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3

R RodBinding[VariantContext]  NA


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GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.