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