Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.


meharmehar Posts: 33Member


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?




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