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terestahlterestahl karolinska InstitutetMember

I am using dbsnp_146.hg38.vcf to annotate my variants with AllleleFrequency "CAF" and I use the command:

java -jar /home/teresita/Programs/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar \
-T VariantAnnotator \
-R /home/teresita/Downloads/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa \
-V haplotypecaller_P4552_109R.vcf.snpEff.ann.vep.ann.vcf \
--resource:foo /home/teresita/Downloads/Broad_bundle_b38/dbsnp_146.hg38.vcf \
--expression foo.CAF --resourceAlleleConcordance \
-o haplotypecaller_P4552_109R.vcf.snpEff.ann.vep.ann.CAF.vcf

However many of my variants get the wrong CAF value, in this example the variant in the sample is T and get CAF=1 that is the value for C
chr4 141588377 rs529748580 C T 532.77 . AC=1;AF=0.500;AN=2;ANN=T|intergenic_region|MODIFIER|RP11-208N20.1-IL15|ENSG00000250141-ENSG00000164136|intergenic_region|ENSG00000250141-ENSG00000164136|||n.141588377C>T||||||;BaseQRankSum=2.89;CSQ=T|intergenic_variant|MODIFIER|||||||||||||||rs529748580||||SNV|||||||||||||||0.0000|||||||||||||||||||1KG_ALL:T:0||||||||;ClippingRankSum=0.00;DB;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.02;ReadPosRankSum=-2.550e-01;SOR=0.675;foo.CAF=1 GT:AD:DP:GQ:PL 0/1:18,20:38:99:561,0,386

This variant appears in dbsnp_146.hg38.vcf like this: chr4 141588377 rs529748580 C T . . RS=529748580;RSPOS=141588377;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000026000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=1,0;COMMON=0

Is it something wrong in my command/understanding? Than you for your help


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    So, it looks like the second value of CAF is being omitted in the output VCF. That is odd. Can you try with the latest version of GATK3 or with GATK4 latest version?


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