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SNV gets dbSNP annotation in one sample, doesn't get annotated in another one
I recently run HaplotypeCaller for GATK3.7 on a series of samples (several GATK runs performed at the same time), using the latest release of dbSNP(150). This was the command line I used for both cases (I omissed the full paths for privacy concerns):
\ -Xmx4g -jar /data01/Softwares/GATK/3.7/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R /path/to/hg19 \
-I input_bam \
-o output.vcf \
and here's the same variant reported in two different files of the same data (exomes) performed using the same kit, on the same NextSeq run
chr11 125479363 rs2241502 G A 208.01 . AC=2;AF=1.00;AN=2;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=23.11;SOR=0.892 GT:AD:DP:GQ:PL 1/1:0,9:9:27:222,27,0
chr11 125479363 . G A 597.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.140;ClippingRankSum=0.000;DP=41;ExcessHet=3.0103;FS=2.820;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.58;ReadPosRankSum=-1.110;SOR=0.448 GT:AD:DP:GQ:PL 0/1:16,25:41:99:605,0,343
I've seen this error running sistematically for several other positions in the same run, and I fear that the error might be always been there and I didn't notice before. I'm wondering if you know why this occurs, if it's a bug and it is known and if I should reannotate with VariantAnnotator every vcf I got in order to fix the issue (if VariantAnnotator is immune from this bug)
Thanks a lot for your help and time, I'm here for every clarification