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Variant Discovery in High-Throughput Sequencing Data

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Can't use GATK or Picard's LiftoverVcf tool without encountering output format exception



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    Bhanu Gandham



    It looks like you provided a txt file in the REJECT argument, which should be a vcf file. Try

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    A S


    Bhanu Gandham Great, thanks, that seems to have worked. But now I am getting another error:

    java.lang.IllegalStateException: Key LowQual found in VariantContext field FILTER at 1:10014 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
    at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(
    at htsjdk.variant.vcf.VCFEncoder.getFilterString(
    at htsjdk.variant.vcf.VCFEncoder.write(
    at htsjdk.variant.variantcontext.writer.VCFWriter.add(
    at picard.vcf.LiftoverVcf.rejectVariant(
    at picard.vcf.LiftoverVcf.doWork(
    at picard.cmdline.CommandLineProgram.instanceMain(
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(
    at org.broadinstitute.hellbender.Main.mainEntry(
    at org.broadinstitute.hellbender.Main.main(


    I think this is because many of the SNPs have a "LowQual" value in one of the fields like so:

    1 6512957 . A . 26.08 LowQual AC=0;AF=0.00;AN=2;DP=21;MQ=28.76;MQ0=4;1000gALT=A;AF1000g=0.01;AFR_AF=0.03;RM;TS=HPGOM;TSseq=A,A,A,A,A;CAnc=A;GAnc=A;OAnc=A;bSC=788;pSC=0.026;GRP=-0.854; Map20=0 GT:DP:GQ:PL:A:C:G:T:IR 0/0:21:1.48:4,0,362:2,18:0,0:0,0:0,1:0

    Now what do I do about this problem? Should I remove the "LowQual" value? The VCF is low quality because that is the nature of the sample; it is from the remains of an Altai Neanderthal.


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    Bhanu Gandham

    This looks like a malformed vcf. I recommend either recreating this vcf or running some validations tests on it using

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    Brian Wiley

    Anyway the error message can indicate which it is for.  People will see this and think error to -O param when it is the --REJECT param is issue.

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    Genevieve Brandt (she/her)

    Hi Brian,

    Thank you for the feedback. In this case, the reject file is an output file type, and so that is why the error message is as written.



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