Left-aligns indels from reads in a bam file.

Category Sequence Data Processing Tools

Traversal ReadWalker

PartitionBy READ


LeftAlignIndels is a tool that takes a bam file and left-aligns any indels inside it. The same indel can often be placed at multiple positions and still represent the same haplotype. While a standard convention 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.


A bam file to left-align.


A left-aligned bam.


 java -Xmx3g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T LeftAlignIndels \
   -I input.bam \
   -o output.vcf

Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by LeftAlignIndels.

Downsampling settings

This tool does not apply any downsampling by default.

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).

LeftAlignIndels 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
Optional Outputs
stdout Output bam

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

Output bam

GATKSAMFileWriter  stdout

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA