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Bad input: Values for QD annotation not detected for ANY training variant in the input callset.

songsysongsy University of MichiganMember
edited August 2014 in Ask the GATK team

Here is my command:

java -jar -Djava.io.tmpdir=temp -Xmx4g GenomeAnalysisTK.jar -T VariantRecalibrator -R human_g1k_v37.fasta -input HGDP00456.raw.SNPs.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_138.b37.vcf \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an DP -mode SNP -recalFile HGDP00456.raw.SNPs.recal \
-tranchesFile HGDP00456.raw.SNPs.tranches -rscriptFile HGDP00456.snp.plots.R

But I'm getting following 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. See http://gatkforums.broadinstitute.org/discussion/49/using-variant-annotator

I have never got such errors before. Also note that, the vcf file I'm using is a little bit different than before. I'm running haplotypecaller with -ERC GVCF. After I got the gvcf file, I use gvcftools to make vcf files(only keep the snp) and then use vcf-merge to make a single variant vcf file. I also remove the NON_REF tag in the ALT filed.

Here is the vcf file:

1       13975   .       A       T       97.77   .       BaseQRankSum=0.729;ClippingRankSum=0.361;DP=10;MLEAC=1,0;MLEAF=0.500,0.00;MQ=28.54;MQ0=0;MQRankSum=-0.361;ReadPosRankSum=-0.361 GT:AD:DP:GQ:PL:SB       0/1:4,5,0:9:78:126,0,78,138,93,231:3,1,2,3
1       14673   rs369473859     G       C       1.69    .       BaseQRankSum=0.762;ClippingRankSum=0.067;DB;DP=10;MLEAC=1,0;MLEAF=0.500,0.00;MQ=20.73;MQ0=0;MQRankSum=0.762;ReadPosRankSum=0.067        GT:AD:DP:GQ:PL:SB       0/1:7,2,0:9:25:25,0,150,46,156,202:4,3,2,0
1       14907   rs79585140      A       G       375.77  .       BaseQRankSum=2.059;ClippingRankSum=0.686;DB;DP=29;MLEAC=1,0;MLEAF=0.500,0.00;MQ=30.17;MQ0=0;MQRankSum=-1.970;ReadPosRankSum=-1.173      GT:AD:DP:GQ:PL:SB       0/1:12,17,0:29:99:404,0,265,440,316,756:8,4,12,5
1       14930   rs75454623      A       G       504.77  .       BaseQRankSum=-2.029;ClippingRankSum=0.787;DB;DP=40;MLEAC=1,0;MLEAF=0.500,0.00;MQ=28.38;MQ0=0;MQRankSum=-1.118;ReadPosRankSum=0.897      GT:AD:DP:GQ:PL:SB       0/1:16,24,0:40:99:533,0,341,581,413,994:11,5,16,8
1       15211   rs78601809      T       G       22.79   .       BaseQRankSum=-1.026;ClippingRankSum=0.000;DB;DP=4;MLEAC=1,0;MLEAF=0.500,0.00;MQ=27.99;MQ0=0;MQRankSum=1.026;ReadPosRankSum=-1.026       GT:AD:DP:GQ:PL:SB       0/1:2,2,0:4:41:52,0,41,59,47,106:0,2,0,2
1       15820   rs200482301     G       T,GCTT  6.08    .       DB;DP=3;MLEAC=2,0,0;MLEAF=1.00,0.00,0.00;MQ=27.15;MQ0=0 GT:AD:DP:GQ:PL:SB       1/1:0,2,0,0:2:6:71,9,0,52,6,90,46,6,49,43:0,0,0,0

However, when I ran VQSR on this vcf file. I have above errors. I'm using latest GATK v3.2.2, and I also tried earlier version 2.8, same error.

I wonder what I'm doing wrong. Thanks!!


  • songsysongsy University of MichiganMember

    I guess I'm just asking, how can I perform VQSR on the gvcf after HaplotypeCaller. If I extract the variants(non-ref ones) from gvcf and merge them together into a vcf file. Can I perform VQSR on that?? I just don't want to do normal haplotypeCaller again.....

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    If you're using -ERC GVCF mode, you need to run GenotypeGVCFs on your GVCF files, which are only meant to be intermediates until joint genotyping. Then you can perform VQSR on the VCF output by GenotypeGVCFs. The QD annotation should be added in this second step. If it's not you can run VariantAnnotator to add it.

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