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How can i use the optional tool; OUTPUT_VCF?

NobuhikoNobuhiko Member
edited September 2018 in Ask the GATK team


How can i use the optional tool; OUTPUT_VCF?
I saw https://software.broadinstitute.org/gatk/documentation/tooldocs/
I entered below command.
However, i couldn't get the VCF.file. I could get only three files; oncordance_contingency_metrics, oncordance_detail_metrics, oncordance_summary_metrics.

java -jar picard.jar GenotypeConcordance \
CALL_VCF=input.vcf \
CALL_SAMPLE=sample01 \
O=concordance.vcf \
TRUTH_VCF=Ref.vcf \
TRUTH_SAMPLE=sample02 \

How can i get the VCF file?
Thank you.

Best Answers


  • Dear Daniel.

    Thanks for answering me. I was able to do it with your help.
    Thank you very much.


  • Dear,

    I could get "concordance.vcf" file, but it contained only chr1 and chr2 data.
    What's happened? And how can I get all the data.
    Thank you.

    Best Regard,

    java -jar picard.jar GenotypeConcordance \TRUTH_VCF=sample1.vcf \TRUTH_SAMPLE=sample1 \CALL_VCF=sample2.vcf \CALL_SAMPLE=sample2 \O=concordance.vcf \OUTPUT_VCF=true

    INFO 2018-09-28 14:58:00 GenotypeConcordance checked 660,000 variants. Elapsed time: 00:00:39s. Time for last 10,000: 0s. Last read position: chr2:168,888,882

    [Fri Sep 28 14:58:00 JST 2018] picard.vcf.GenotypeConcordance done. Elapsed time: 0.64 minutes.
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" java.lang.IllegalArgumentException: Features added out of order: previous (TabixFeature{referenceIndex=1, start=170702011, end=170702011, featureStartFilePosition=1626752176963, featureEndFilePosition=-1}) > next (TabixFeature{referenceIndex=1, start=170702008, end=170702011, featureStartFilePosition=1626752177151, featureEndFilePosition=-1})
    at htsjdk.tribble.index.tabix.TabixIndexCreator.addFeature(TabixIndexCreator.java:89)
    at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.add(IndexingVariantContextWriter.java:203)
    at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:240)
    at picard.vcf.GenotypeConcordance.writeVcfTuple(GenotypeConcordance.java:527)
    at picard.vcf.GenotypeConcordance.lambda$doWork$0(GenotypeConcordance.java:396)
    at java.util.Optional.ifPresent(Optional.java:159)
    at picard.vcf.GenotypeConcordance.doWork(GenotypeConcordance.java:396)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

  • NobuhikoNobuhiko Member
    Accepted Answer

    Sorry for not replying for a long time.
    I'm really thankful to you. I managed to do it.

    I really appreciate your help.

    Best Regars,
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin


    I am glad you were able to figure it out. If possible please post your solution so that the community can benefit from it too.

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