DP for INDEL is more than 100 and AD is 0
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.