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Error in SortVcf

I have been going through this problem. Is this very common and is there any solution to this error.

Exception in thread "main" java.lang.IllegalStateException: Key . found in VariantContext field INFO at 10:153837 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(VCFEncoder.java:173)
at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:112)
at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:224)
at picard.vcf.SortVcf.writeSortedOutput(SortVcf.java:187)
at picard.vcf.SortVcf.doWork(SortVcf.java:105)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @abiskargyawali
    Hi,

    Have a look at this thread. Are you using the latest version of GATK3?

    Thanks,
    Sheila

  • Hi Sheila
    I have been using GATK3. Here is what i did

    java -Xmx100g -jar picard.jar SortVcf
    I=Input.vcf
    O=sorted.vcf
    SEQUENCE_DICTIONARY=Zea_mays.AGPv3.28.dna.genome.dict

    This is the error that i got

    Exception in thread "main" java.lang.IllegalStateException: Key . found in VariantContext field INFO at 10:153837 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(VCFEncoder.java:173)
    at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:112)
    at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:224)
    at picard.vcf.SortVcf.writeSortedOutput(SortVcf.java:187)
    at picard.vcf.SortVcf.doWork(SortVcf.java:105)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

    Looking at the position 10:153837, i did not find any thing different from other sites.

    fileformat=VCFv4.0

    Tassel=<ID=GenotypeTable,Version=5,Description="Reference allele is not known. The major allele was used as reference allele">

    FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

    FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the reference and alternate alleles in the order listed">

    FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">

    FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">

    FORMAT=<ID=PL,Number=.,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">

    INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">

    INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">

    INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

    10 153837 S10_153837 G A . PASS .;DP=3672 GT:AD:DP:GQ:PL

    I dont know what is going on over here. Any help would be appreciated.

    Thanks
    Abi

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @abiskargyawali
    Hi Abi,

    How did you produce the input VCF? Did you use HaplotypeCaller? If so, do you still get the error if you use version 3.8?

    Thanks,
    Sheila

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