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# LiftoverVariants

Member Posts: 101

Hi,

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?

Thanks.

Tagged:

I believe you need the new build reference.

Geraldine Van der Auwera, PhD

• Member Posts: 101

Okay. Will try and get back if there is any problem. Thanks

• Member Posts: 6

Hi Dr. Van der Auwera,

I am trying to convert a vcf file from rn4 to rn5 (rat vcf files)
0) Where might I find LiftoverVariants.jar. Is it not part of GATK v2.6-5? I looked for documentation, but I couldn't find. Looked at ftp.broadinstitute.org. I did spend some time looking for, sorry if it is under my nose.

1) Are the UCSC chains for non-humans going to work?

Thank you very much.

Hi Drepanis,

The liftover tools are packaged within the GATK jar, as are all our tools. We don't make separate jars like the Picard tools, if that's what you were thinking of.

I can't comment on the rat chain files but I expect they should work fine, yes.

Geraldine Van der Auwera, PhD

• TNMember Posts: 28
edited June 2015

I have run into errors at the second step of the two steps of lifting b37 vcf to hg19 (shows simplified commands below).

the first step seems fine (but headers did not changed to hg19!!!) to lift over b37 to hg19:
java -jar GenomeAnalysisTK.jar -T LiftoverVariants -R GRCh37.fa -chain b37tohg19.chain -dict hg19.dict -V dedup.vcf.gz -o dedup.hg19.vcf.gz.temp

then the second step that filters variants has the error (supplied with b37 reference will also show errors):
java -jar GenomeAnalysisTK.jar -T FilterLiftedVariants -R hg19.fa -V dedup.hg19.vcf.gz.temp -o dedup.hg19.vcf.gz