Left-aligns indels from a variants file.
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.
A variant set to left-align and trim.
A left-aligned VCF.
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.
This tool applies the following downsampling settings by default.
This tool uses a sliding window on the reference.
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).
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|
|NA||Input VCF file|
|stdout||File to which variants should be written|
|false||Split multiallelic records and left-align individual alleles|
|false||Trim alleles to remove bases common to all of them|
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.
File to which variants should be written
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.
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.
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).
GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA