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Wrong results with QD,bug?

ZexuanZexuan JiangsuChinaMember
edited June 2017 in Ask the GATK team

@valentin @Geraldine_VdAuwera
Hello, I do HaplotypeCaller twice,then compared the result vcf files with notepad++ plugin Compare.I found some different value about the QD annotation:

java -Xmx12G -jar $gatk -T HaplotypeCaller -R $fasta -I $data/sra/SRR948862/SRR948862.recal.bam -D $dbsnp --genotyping_mode DISCOVERY -o $data/sra/SRR948862/SRR948862.vcf -nct 12
-nct 12 : 12 threads,bigger than one!!!
image
chrM 12706 rs267606893 T C 6851.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.963;ClippingRankSum=0.000;DB;DP=194;ExcessHet=3.0103;FS=3.313;MLEAC=2;MLEAF=1.00;MQ=59.39;MQRankSum=-0.210;QD=33.85;ReadPosRankSum=0.342;SOR=0.461 GT:AD:DP:GQ:PL 1/1:1,192:193:99:6880,544,0
chrM 12706 rs267606893 T C 6851.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.963;ClippingRankSum=0.000;DB;DP=194;ExcessHet=3.0103;FS=3.313;MLEAC=2;MLEAF=1.00;MQ=59.39;MQRankSum=-0.210;QD=27.78;ReadPosRankSum=0.342;SOR=0.461 GT:AD:DP:GQ:PL 1/1:1,192:193:99:6880,544,0
we know QD=QUAL/AD(https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_annotator_QualByDepth.php),but they all wrong,and right with same value.

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