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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?