Hi team,
I'm have a vcf callset file generated using HaplotypeCaller in --emitRefConfidence GVCF mode with subsequent GenotypeGVCFs.
I used the generated output.vcf file as input for VariantRecalibration
The command:
java -jar $GATK_HOME/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R $REFERENCE \ -input exome_set_output.vcf \ -resource:hapmap,known=false,training=true,truth=true,prior=15.0 $GOLD_STANDARD_HAPMAP \ -resource:omni,known=false,training=true,truth=true,prior=12.0 $GOLD_STANDARD_OMNI \ -resource:1000G,known=false,training=true,truth=false,prior=10.0 $GOLD_STANDARD_1000G \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 $GOLD_STANDARD_DBSNP \ -an DP -an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum -an InbreedingCoeff \ -mode SNP \ -tranche 100.0 -tranche 99.9 \ -recalFile exome_set_output_SNP.recal \ -tranchesFile recal_SNP.tranches \ -rscriptFile recal_SNP_plots.R \
But I get the following error:
##### ERROR MESSAGE: Bad input: Values for DP annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
My input vcf file looks like this:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RTN005 RTN007 RTN009 RTN024 RTN028 RTN038 RTN039 RTN045 RTN051 RTN097 RTN102 RTN108 RTN122 RTN126 RTN127 RTN133 1 762273 . G A 23942.06 . AC=31;AF=0.969;AN=32;BaseQRankSum=-9.420e-01;ClippingRankSum=-6.500e-02;DP=743;FS=2.053;GQ_MEAN=139.56;GQ_STDDEV=44.68;InbreedingCoeff=-0.0323;MLEAC=31;MLEAF=0.969;MQ=42.48;MQ0=0;MQRankSum=-2.517e+00;NCC=0;QD=32.27;ReadPosRankSum=-1.485e+00 GT:AD:DP:GQ:PL 1/1:0,42:42:99:1426,126,0 1/1:0,28:28:84:945,84,0 1/1:0,69:69:99:2430,208,0 1/1:0,38:38:99:1295,114,0 1/1:0,54:54:99:1876,162,0 1/1:0,28:28:84:977,84,0 1/1:0,37:37:99:1282,111,0 1/1:0,65:65:99:2207,195,0 1/1:0,46:46:99:1572,138,0 1/1:0,45:45:99:1565,135,0 1/1:0,60:60:99:2019,180,0 1/1:0,52:52:99:1758,156,0 1/1:0,69:69:99:2404,208,0 1/1:0,19:19:57:657,57,0 1/1:0,41:41:99:1413,123,0 0/1:40,9:49:99:152,0,1320 1 762353 . G C 59.07 . AC=1;AF=0.031;AN=32;BaseQRankSum=0.111;ClippingRankSum=-5.560e-01;DP=321;FS=0.000;GQ_MEAN=51.81;GQ_STDDEV=19.63;InbreedingCoeff=-0.0328;MLEAC=1;MLEAF=0.031;MQ=42.47;MQ0=0;MQRankSum=0.779;NCC=0;QD=1.97;ReadPosRankSum=0.501 GT:AD:DP:GQ:PL 0/0:22,0:22:63:0,63,945 0/0:23,0:23:60:0,60,832 0/0:15,0:15:23:0,23,574 0/0:22,0:22:60:0,60,900 0/0:26,0:26:63:0,63,945 0/0:8,0:8:21:0,21,303 0/0:15,0:15:42:0,42,489 0/0:26,0:26:60:0,60,900 0/0:11,0:11:30:0,30,450 0/0:23,0:23:63:0,63,945 0/1:25,5:30:95:95,0,783 0/0:23,0:23:60:0,60,900 0/0:29,0:29:63:0,63,945 0/0:20,0:20:60:0,60,685 0/0:15,0:15:36:0,36,540 0/0:13,0:13:30:0,30,450 1 861630 . G A 1958.44 . AC=22;AF=0.688;AN=32;BaseQRankSum=-1.380e+00;ClippingRankSum=0.198;DP=88;FS=7.101;GQ_MEAN=24.38;GQ_STDDEV=23.34;InbreedingCoeff=0.0754;MLEAC=25;MLEAF=0.781;MQ=60.00;MQ0=0;MQRankSum=0.00;NCC=0;QD=25.43;ReadPosRankSum=0.720 GT:AD:DP:GQ:PL 0/0:3,0:3:0:0,0,51 0/1:4,2:6:46:46,0,146 1/1:0,4:4:12:133,12,0 1/1:0,4:4:12:133,12,0 1/1:0,6:6:18:197,18,0 1/1:0,2:2:6:64,6,0 1/1:0,7:7:21:209,21,0 1/1:0,8:8:24:264,24,0 1/1:0,7:7:21:232,21,0 0/1:4,3:7:76:76,0,137 0/0:4,0:4:0:0,0,93 0/1:2,4:6:64:113,0,64 0/1:2,5:7:51:135,0,51 1/1:0,10:10:30:321,30,0 1/1:0,3:3:9:100,9,0 0/0:4,0:4:0:0,0,88
Can someone point me to what I'm doing wrong? I can see that there are DP values in the vcf file so I don't understand why it complains there aren't any annotations.
Thanks very much,
Tesa