VariantRecalibrator Error: Values for QD annotation not detected for ANY training variant

nb82nb82 United StatesMember

Hi,
I get the following error with VariantRecalibrator when I run it:

java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Os_nipponbare_v7.0_genome.fasta -input ESSR.vcf -mode SNP -recalFile ERS468243.raw.snps.recal -tranchesFile ERS468243.raw.snps.tranches -rscriptFile ERS468243.recal.plots.R -resource:dbSNP,known=true,training=true,truth=true,prior=6.0 all_sorted.vcf -an QD -an MQRankSum -an ReadPosRankSum -an FS -an MQ

ERROR MESSAGE: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.

What am I doing wrong? Am I using the wrong annotation?
Thanks in advance for any help.
Best,
NB

Best Answer

Answers

  • nb82nb82 United StatesMember

    Hi Sheila, thank you for a prompt response, I really appreciate it. I had a follow-up question. So, if I want to add QD annotation to my input file, does the following command look OK to you:

    java -jar GenomeAnalysisTK.jar -R ref.fasta -T VariantAnnotator -I input.bam -o output_variant_file_with_QD.vcf -A QD --variant input_variant_file_without_QD.vcf -L input_variant_file_without_QD.vcf --dbsnp dbsnp.vcf

    Thanks Sheila,
    NB

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @nb82
    Hi NB,

    That looks great, except the -A argument takes the full name of the annotation. So, inetsad of QD, you will specify QualByDepth.

    -Sheila

  • nb82nb82 United StatesMember
    edited February 2015

    Thanks Sheila for the prompt answer again. I really appreciate it.
    However, I went back and looked at my .vcf file created from HaplotypeCaller step and found that it was the culprit. It is not populated; here is a snapshot:

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ERS468243
    Chr1 1 . N . . END=1054 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
    Chr1 1055 . C . . END=1056 GT:DP:GQ:MIN_DP:PL 0/0:2:5:2:0,6,51
    Chr1 1057 . C . . END=1058 GT:DP:GQ:MIN_DP:PL 0/0:2:0:2:0,0,0
    Chr1 1059 . A . . END=1070 GT:DP:GQ:MIN_DP:PL 0/0:2:5:2:0,6,49
    Chr1 1071 . T . . END=1393 GT:DP:GQ:MIN_DP:PL 0/0:1:0:0:0,0,0

    For some reason, it does not list the Ref allele and annotations. I have gone through the entire set of commands and found nothing wrong. Additionally, there is no error/warning in stdout of any of the steps.
    Can you help me figure out what could be the reason for the vcf file above? what are some the usual suspects?
    Thanks,
    NB

  • nb82nb82 United StatesMember
    edited February 2015

    Hi,
    I did a bit more reading and digging, by playing around with the parameters and found that the semi-empty vcf file from HaplotypCaller (v3.2) is produced when I used the -ERC GVCF option. Then I read this post:
    http://gatkforums.broadinstitute.org/discussion/4917/missing-reference-allele-in-gvcf-file-after-running-haplotypecaller

    I realized that the file that I have is normal for GVCF output.

    So, I have another follow-up question which I think should have its own thread for future users. So I will ask it there.
    Thanks in advance,
    NB

    Post edited by nb82 on
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @nb82
    Hi NB,

    I will look out for your new thread!

    -Sheila

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