Left-align indels in a variant callset
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.
A variant call set to left-align and trim.
A left-aligned VCF.
java -jar GenomeAnalysisTK.jar \ -T LeftAlignAndTrimVariants \ -R reference.fasta \ --variant input.vcf \ -o output.vcf
java -jar GenomeAnalysisTK.jar \ -T LeftAlignAndTrimVariants \ -R reference.fasta \ --variant input.vcf \ -o output.vcf \ --dontTrimAlleles
java -jar GenomeAnalysisTK.jar \ -T LeftAlignAndTrimVariants \ -R reference.fasta \ --variant input.vcf \ -o output.vcf \ --reference_window_stop 208
java -jar GenomeAnalysisTK.jar \ -T LeftAlignAndTrimVariants \ -R reference.fasta \ --variant input.vcf \ -o output.vcf \ --splitMultiallelics
java -jar GenomeAnalysisTK.jar \ -T LeftAlignAndTrimVariants \ -R reference.fasta \ --variant input.vcf \ -o output.vcf \ --splitMultiallelics \ --dontTrimAlleles --keepOriginalAC
These Read Filters are automatically applied to the data by the Engine before processing by LeftAlignAndTrimVariants.
This tool uses a sliding window on the reference.
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.
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 |
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.
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
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
File to which variants should be written
VariantContextWriter stdout
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
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