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AD value higher than the DP value

redred Posts: 10Member
edited February 2013 in Ask the GATK team

Calling SNPs using a single bam file with the command:

 java -Xmx30g -jar GenomeAnalysisTK.jar \
 -T UnifiedGenotyper  \
 -R ref.fasta  \
 -I  input.bam  \
 -o output.vcf \

and when looking at the output file, most DP values were equal to the AD values and in few cases the AD value was higher. Thought that AD values are the unfiltered counts of all reads and DP fields describes the total depth of reads that passed the Unified genotyper’s internal quality control. Is it normal for the AD values to be higher than the DP value?

 #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  eo227
 gi|218430358|emb|CU928163.2|    2317180 .       T       G       76.55   .       AC=1;AF=0.50;AN=2;BaseQRankSum=1.568;DP=10;Dels=0.00;FS=11.181;HRun=0;HaplotypeScore=15.8585;MQ=28.63;MQ0=0;MQRankSum=1.036;QD=7.66;ReadPosRankSum=-0.633;SB=-0.01      GT:AD:DP:GQ:PL  0/1:6,4:10:99:107,0,154

 gi|218430358|emb|CU928163.2|    2317181 .       T       G       71.96   .       AC=1;AF=0.50;AN=2;BaseQRankSum=0.550;DP=10;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=19.8574;MQ=28.63;MQ0=0;MQRankSum=-1.754;QD=7.20;ReadPosRankSum=-1.754;SB=-0.01      GT:AD:DP:GQ:PL  0/1:3,4:10:87.90:102,0,88
Post edited by Geraldine_VdAuwera on

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