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I am using GATK v2.4.9 and i am trying to liftover from one build to another. Below are the arguments for LiftoverVariants:
Arguments for LiftoverVariants: -V,--variant Input VCF file -o,--out File to which variants should be written -chain,--chain Chain file -dict,--newSequenceDictionary Sequence .dict file for the new build -recordOriginalLocation,--recordOriginalLocation Should we record what the original location was in the INFO field?
Here is the command i have used, java -jar GenomeAnalysisTK.jar -T LiftoverVariants -chain canFam2ToCanFam3.over.chain -dict canFam3_dog_genome.dict -V canFam2_snp131.vcf -o canFam3_snp131.vcf
It showed an error message: ERROR MESSAGE: Walker requires a reference but none was provided.
The argument reference was not present in the documentation and the tool needs a reference argument. If it is required, what should be the reference file, new build or old build?