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error_Values for InbreedingCoeff annotation not detected for ANY training variant in the input

douymdouym Member
edited August 2012 in Ask the GATK team

Hi, when I run VariantRecalibrator using the following commands:
run_gatk.sh
-T VariantRecalibrator
-R GRCh37/human_g1k_v37.fasta
-input raw4.snp.vcf
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_134.b37.vcf
-an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff -mode SNP
-recalFile raw4.snp.vcf.recal
-tranchesFile raw4.snp.vcf.tranches
-rscriptFile raw4.snp.vcf.plots.R"

error message as follows:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.0-39-gd091f72):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Bad input: Values for InbreedingCoeff annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator

Which kind of annotations should I add and how?
I'm quite worry, thanks a lot!

Best Answer

  • ebanksebanks Broad Institute ✭✭✭✭
    Accepted Answer

    It's good to see that you are working through this problem on your own. Please note that the error message you posted explicitly asks you NOT to post it to this forum since you should be able to figure it out by looking at the documentation available on this site.

Answers

  • douymdouym Member

    I removed "-an InbreedingCoeff" and added --maxGaussians 4 , problem resolved
    don't know if that's good

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
    Accepted Answer

    It's good to see that you are working through this problem on your own. Please note that the error message you posted explicitly asks you NOT to post it to this forum since you should be able to figure it out by looking at the documentation available on this site.

  • airtimeairtime Member

    I have the same error and the documentation and some looks into the raw vcf file shows me that Annotations are missing for some variants. But at the InbreedingCoeff documentations it is not shown which annotations are required, so I don't know which annotation I should add with VariantAnnotator.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @airtime,

    If it is the exact same error (saying that the InbreedingCoeff annotation is missing) then you can try adding that annotation with VariantAnnotator. It doesn't require other annotations. But keep in mind that the InbreedingCoefficient can only be calculated if you have at least 10 samples. If you have fewer samples, then you should remove that annotation from your VariantRecalibrator command.

  • airtimeairtime Member

    Hi Geraldine_VdAuwera,
    thank you. The set which I use contains 27 samples.
    Is the benefit of VariantAnnotator is speed? Or could I use also again the UnifiedGenotyper with the needed Annotation (InbreedingCoeff), because VariantAnnotator needs the bam files as input. What would you suggest?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Both need the bam files, but adding the annotation with VariantAnnotator will be much faster than using UnifiedGenotyper since VA doesn't do all the genotyping calculations that UG does. VA adds annotations to an existing callset while UG makes an entirely new callset. So you should use VariantAnnotator.

  • Hi douym,
    How do you know just removed "-an InbreedingCoeff" is working ?it'smiracle
    he > @douym said:

    I removed "-an InbreedingCoeff" and added --maxGaussians 4 , problem resolved
    don't know if that's good

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @psyche
    Hi,

    Are you having the same error message? I think once the original poster removed InbreedingCoeff as one of the requested annotations in their command, the error went away and the tool ran to completion.

    -Sheila

  • @Geraldine_VdAuwera hi , I have a question ,you told that the InbreedingCoefficient can only be calculated if you have at least 10 samples,but how about other annotations? what is the relationship between the other annotations and sample nummber? where can I find that kind of information?

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @yards112
    Hi,

    I cannot think of any annotations that require the 10 or more samples (other than InbreedingCoeff), but you can read more about the annotations and their requirements here.

    -Sheila

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