LeftAlignIndels

Left-aligns indels from reads in a bam file.

Category Sequence Data Processing Tools

Traversal ReadWalker

PartitionBy READ

Overview

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.

Input

A bam file to left-align.

Output

A left-aligned bam.

Examples

 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.

MalformedReadFilter

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

LeftAlignIndels 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
Optional
--out	StingSAMFileWriter	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 ( StingSAMFileWriter with default value stdout )

Output bam.

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.