Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf --splitMultiallelics --dontTrimAlleles --keepOriginalAC


Manual

Argument name(s)Default valueSummary
Required Inputs
--variant
 -V
NAInput VCF file
Optional Outputs
--out
 -o
stdoutFile to which variants should be written
Optional Flags
--dontTrimAlleles
 -notrim
falseDo not Trim alleles to remove bases common to all of them
--keepOriginalAC
falseStore the original AC, AF, and AN values after subsetting
--splitMultiallelics
 -split
falseSplit multiallelic records and left-align individual alleles


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