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DP for INDEL is more than 100 and AD is 0

Hi all,

I have the below INDEL call from GATK-3.3 Haplotype caller.

chr17   39190954    .   G   GCAGCAGCTTGGCTGGCAGCAGCTGGTCTCA 770.52  PASS    AC=1;AF=0.500;AN=2;DP=138;    
FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;QD=5.58;SOR=0.693   GT:AD:DP:GQ:PL  0/1:0,0:0:7:807,0,7

The command used:

java -Xmx10G -jar GenomeAnalysisTK.jar -R %s -T HaplotypeCaller -I %s -L %s -stand_emit_conf 10 -stand_call_conf 30     
--genotyping_mode DISCOVERY -o %s

DP in the INFO field is 138 and AD from the FORMAT field is 0,0. I understand that DP and AD are unfiltered and filtered depths. However, having 0 reads is something alarming. Could someone help me to understand the differing read depths.

Best Answer


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