java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf
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 |