The front line support team will be unavailable to answer questions until May 27th 2019 as we are celebrating Memorial Day. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

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!!!
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(,but they all wrong,and right with same value.


Best Answer


Sign In or Register to comment.