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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?



Best Answer


  • meharmehar Member ✭✭

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

  • DrepanisDrepanis Member

    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.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    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.

  • 5581681555816815 TNMember
    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

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.4-0-g7e26428):
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR MESSAGE: Input files dedup.hg19.vcf.gz.temp and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
    ERROR dedup.hg19.vcf.gz.temp contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]
    ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
    ERROR ------------------------------------------------------------------------------------------
  • SheilaSheila Broad InstituteMember, Broadie admin


    Did you use the right hg19.fa file? It looks like the vcf does not have a lot of the contigs present in the vcf.


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