I generate a vcf with bp resolution using following command with GATK 3.7
$ java -jar ~/Downloads/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19.fasta -I NA03403.bam -o NA03403_1_variants37.bp.vcf -L 15:91310129-91310263 -bamout bamout_37_NA03403_1.bam --genotyping_mode DISCOVERY --emitRefConfidence BP_RESOLUTION
My output looks like this -
15 91310136 . T . . . GT:AD:DP:GQ:PL 0/0:690,0:690:99:0,120,1800
15 91310137 . T . . . GT:AD:DP:GQ:PL 0/0:693,0:693:99:0,120,1800
15 91310138 . A . . . GT:AD:DP:GQ:PL 0/0:697,0:697:99:0,120,1800
15 91310139 . G . . . GT:AD:DP:GQ:PL 0/0:693,0:693:99:0,120,1800
15 91310140 . A . . . GT:AD:DP:GQ:PL 0/0:696,0:696:99:0,120,1800
15 91310141 . T . . . GT:AD:DP:GQ:PL 0/0:695,0:695:99:0,120,1800
15 91310142 . T . . . GT:AD:DP:GQ:PL 0/0:684,1:685:0:0,0,0
15 91310143 . C . . . GT:AD:DP:GQ:PL 0/0:675,0:675:0:0,0,0
15 91310144 . C . . . GT:AD:DP:GQ:PL 0/0:666,0:666:0:0,0,0
15 91310145 . A . . . GT:AD:DP:GQ:PL 0/0:663,0:663:0:0,0,0
15 91310146 . G . . . GT:AD:DP:GQ:PL 0/0:656,0:656:0:0,0,0
15 91310147 . C . . . GT:AD:DP:GQ:PL 0/0:648,0:648:0:0,0,0
15 91310148 . T . . . GT:AD:DP:GQ:PL 0/0:640,0:640:0:0,0,0
15 91310149 . A . . . GT:AD:DP:GQ:PL 0/0:627,0:627:0:0,0,0
15 91310150 . C . . . GT:AD:DP:GQ:PL 0/0:611,6:617:0:0,0,0
15 91310151 . A . . . GT:AD:DP:GQ:PL 0/0:583,27:610:0:0,0,0
15 91310152 . TATC T, 32325.73 . DP=712;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=3285019.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,693,0:693:99:0|1:91310152_TATC_T:32363,2176,0,32364,2176,32364:0,0,481,212
15 91310153 . A . . . GT:AD:DP:GQ:PL 0/0:17,520:537:0:0,0,0
15 91310154 . T . . . GT:AD:DP:GQ:PL 0/0:469,4:473:6:0,6,90
15 91310155 . C . . . GT:AD:DP:GQ:PL 0/0:0,466:466:0:0,0,0
15 91310156 . T TA, 33001.73 . DP=711;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=3265388.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,703,0:703:99:0|1:91310152_TATC_T:33039,2221,0,33039,2221,33039:0,0,486,217
15 91310157 . G . . . GT:AD:DP:GQ:PL 0/0:9,466:475:0:0,0,0
15 91310158 . A ATTC, 33682.73 . DP=721;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=3305298.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,711,0:711:99:0|1:91310152_TATC_T:33720,2275,0,33721,2276,33721:0,0,480,231
15 91310159 . C . . . GT:AD:DP:GQ:PL 0/0:14,619:633:0:0,0,0
15 91310160 . A . . . GT:AD:DP:GQ:PL 0/0:656,1:657:99:0,120,1800
15 91310161 . G . . . GT:AD:DP:GQ:PL 0/0:665,1:666:99:0,120,1800
15 91310162 . G . . . GT:AD:DP:GQ:PL 0/0:670,0:670:99:0,120,1800
15 91310163 . T . . . GT:AD:DP:GQ:PL 0/0:682,0:682:99:0,120,1800
15 91310164 . G . . . GT:AD:DP:GQ:PL 0/0:689,1:690:99:0,120,1800
15 91310165 . A . . . GT:AD:DP:GQ:PL 0/0:704,0:704:99:0,120,1800
15 91310166 . T . . . GT:AD:DP:GQ:PL 0/0:706,1:707:99:0,120,1800
15 91310167 . A . . . GT:AD:DP:GQ:PL 0/0:720,2:722:99:0,120,1800
15 91310168 . A . . . GT:AD:DP:GQ:PL 0/0:737,0:737:99:0,120,1800
My question is why GQ is zero for bases around where ins del are found ?
Thanks !