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Why DP in FORMAT filed can't be re-annotate base on input bam file by Variantannotator?

When I run VariantAnnotator by the follow command(GATK 3.6):

java -Xmx8g -jar GenomeAnalysisTK.jar -R ./hg19.fa -T VariantAnnotator -I ./s733.RG.RA.RC.bam -A BaseQualityRankSumTest -A ClippingRankSumTest -A Coverage -A FisherStrand -A LikelihoodRankSumTest -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest -A TandemRepeatAnnotator -A BaseCounts -A AlleleBalance -A VariantType -A DepthPerAlleleBySample -A DepthPerSampleHC -o ./s733.ReAnno2.vcf --variant ./s733.raw.vcf -L ./s733.raw.vcf --dbsnp./dbsnp_138.hg19.vcf

I got warnings:

WARN 13:50:14,448 AnnotationUtils - DP annotation will not be calculated, must be called from HaplotypeCaller or MuTect2, not VariantAnnotator

What does it mean?

I check the result and found that:

chr1 16374994 rs1889788 C T 2330.77 . ABHom=0.991;AC=2;AF=1.00;AN=2;BaseCounts=0,1,0,107;BaseQRankSum=-0.263;DB;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.78;MQ0=0;MQRankSum=1.824;OND=9.259e-03;QD=21.58;ReadPosRankSum=0.963;SOR=1.117;VariantType=SNP GT:AD:DP:GQ:PL 1/1:1,107:71:99:2359,213,0



DP is not equal to DP in INFO filed, and AD is not equal to DP( 1+107 != 71).

Why this happen? It seems not correct.

Could you please help me with these problem?

Best Answers


  • zhoujj2013zhoujj2013 HongKongMember

    Hi @shlee, thanks.

    As I observed in the output of Variantannotator, Variantannotator never change DP value in FORMAT field. Could you please give me some explanation about this issue? After I got the raw result form HaplotypeCaller, then I want to re-annotate the variant by the input bam file, but I found the DP value in FORMAT field is not consistent with the observed one in input bam file. Is any tools can be used to correct this problem?

  • zhoujj2013zhoujj2013 HongKongMember

    Hi @Geraldine_VdAuwera,

    Is there any software or modules in GATK can generate this metrics (such DP, AD) base on the provided bam file?
    Because Variantannotator generate other metrics(MQ etc.) base on the provided bam file, it's necessary to know the exact DP, AD for each variant, then design hard filter scheme for raw variants.

    Do you think this is the right procedure?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    The HaplotypeCaller will annotate those metrics during the variant calling process. Where does your callset come from?
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