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Left-align indels within reads in a bam file

Category Sequence Data Processing Tools

Traversal ReadWalker

PartitionBy READ


This tool left-aligns any indels within read cigars in order to standardize representation when there are multiple valid representations possible (i.e. where the same indel can be placed at multiple positions and still represent the same haplotype). The standard convention is to place an indel at the left-most position possible, but this is not always followed, so this tool can be used to correct the representation of indels.


This is only really needed when calling variants with legacy locus-based tools such as UnifiedGenotyper. With more sophisticated tools (like HaplotypeCaller) that involve reconstructing haplotypes (eg through haplotype assembly), the problem of multiple valid representations is handled internally and does not need to be corrected explicitly.


A bam file with mapped reads.


A bam file in which indels have been left-aligned where appropriate.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -R reference.fasta \
   -T LeftAlignIndels \
   -I reads.bam \
   -o output_with_leftaligned_indels.bam

Additional Information

Read filters

These Read Filters are 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

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.

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

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.