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CountFalsePositives tool

Helow everyone,
I am using v and trying to count the FP in my VCF file and I have used the following command:
"gatk CountFalsePositives -V $V -R $REF -O false-positives.txt"

And I got the following error:

"org.broadinstitute.hellbender.exceptions.GATKException: Cannot call getTraversalParameters() without specifying either intervals to include or exclude.
at org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection.getTraversalParameters(IntervalArgumentCollection.java:151)
at org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection.getIntervals(IntervalArgumentCollection.java:111)
at org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositives.onTraversalSuccess(CountFalsePositives.java:85)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1041)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
"

May anyone help me to solve that?

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Sakhaa

    Which version of gatk are you using?

  • SakhaaSakhaa Member
    Hi @bhanuGandham
    gatk 4.1.2.0
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    @Sakhaa

    Please validate your vcf with ValidateVariants.

  • SakhaaSakhaa Member
    Hello @bhanuGandham

    I have used the following command
    gatk ValidateVariants -R $REF -V $V --dbsnp $dbsnp

    and I got the following bug
    "20:00:24.989 INFO ProgressMeter - GL000192.1:155718 13.5 4768614 354125.2
    20:00:24.989 INFO ProgressMeter - Traversal complete. Processed 4768614 total variants in 13.5 minutes.
    20:00:24.989 INFO ValidateVariants - Shutting down engine
    "
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @Sakhaa

    Can you please provide an intervals list with this command and try again to see if that resolves the issue?

  • tsato3tsato3 Cambridge, MAMember, Broadie, Dev

    Hi @Sakhaa thanks for reporting this. CountFalsePositives requires an intervals file. I made a PR to make this requirement explicit. https://github.com/broadinstitute/gatk/pull/6120

  • SakhaaSakhaa Member

    thank you @tsato3 and @bhanuGandham

    I still go an error

    A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "chr2:1-100 " is not valid for this input.

    and my comment is the following:

    gatk CountFalsePositives -V total_chroms.snp.recal.vcf.gz -R human_g1k_v37.fasta --intervals var.list -O false-positives_ch20.txt

    could anyone help me in that?

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Sakhaa

    We are not monitoring questions posted on the forum at this time and cannot guarantee a response. Our team is out of office until Jan 2nd 2020. If you are not able to find a solution, please post your question again after Jan 2nd.

  • SakhaaSakhaa Member

    Thank you @bhanuGandham

    I still got an error

    A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "chr2:1-100 " is not valid for this input.

    and my comment is the following:

    gatk CountFalsePositives -V total_chroms.snp.recal.vcf.gz -R human_g1k_v37.fasta --intervals var.list -O false-positives_ch20.txt

    could anyone help me in that?

  • DerekCADerekCA Member, Administrator, Broadie, Moderator admin

    Thanks for returning to the question, @Sakhaa. We're looking into the error, now.

  • DerekCADerekCA Member, Administrator, Broadie, Moderator admin
    edited January 6

    @Sakhaa Your error is likely to be a result of the intervals file being in the wrong format. Please check that your intervals file is in the proper format!

    A common error might be that the fields are not separated by tabs, or the genome coordinates are 0-based and not 1-based.

    If that doesn't work, please let me know.

    Post edited by DerekCA on
  • DerekCADerekCA Member, Administrator, Broadie, Moderator admin

    Okay, Sakhaa. I have several theories for you that may require more work on your part. Please try and fix these things one at a time to see if you can isolate the issue.

    (1) First of all, you may be receiving an error because the tool is not finding "chr2:1-100", and is expecting it to be in the "2:1-100" format. Try removing "chr" and see if that works.

    (2) The second theory is that you have extra white space in the interval file. Check to make sure that there are no hanging spaces and see if that fixes the issue.

    (3) You may also find a solution at the following link, in regards to a discrepancy in your human reference. https://gatkforums.broadinstitute.org/gatk/discussion/23390/grch37-hg19-b37-humang1kv37-human-reference-discrepancies

    (4) If the previous three theories don't solve your problem, then we would be interested in you pasting your sequence dictionaries for your files to see if we can dig around and see what else is causing it. There may be an issue in the sequence validation reference that is leading to the error.

    If you have further questions, I suggest you follow up by making a new forum post so others can give input.

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