Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

How can i use the optional tool; OUTPUT_VCF?

NobuhikoNobuhiko Member
edited September 2018 in Ask the GATK team

Dear,

How can i use the optional tool; OUTPUT_VCF?
I saw https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.5.0/picard_vcf_GenotypeConcordance.php.
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 \
OUTPUT_VCF=output.vcf

How can i get the VCF file?
Thank you.

Best Answers

Answers

  • Dear Daniel.

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

    Sincerely,
    Nobuhiko

  • 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,
    Nobuhiko


    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.
    Runtime.totalMemory()=145227776
    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
    Dear,

    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,
    Nobuhiko
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    @Nobuhiko

    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.

Sign In or Register to comment.