DP field seems off after GenotypeGVCFs

Hello,

I am merging a large number of gvcfs in batches and everything looks fine except the DP field. In some samples the DP field is not present in the gvcf files (see below) and therefore when merging all samples some of the samples have a . (DOT) in the DP field because it is not present in the gvcf file. Main problem is that when in later analysis filtering for DP than all the . (DOT) variants are removed... Is there a way to solve this problem without remaking all the gvcf files?

Thanks & Regards, Floris

gVCF file 1:

3   148896153   .   A   <NON_REF>   .   .   END=148896155   GT:DP:GQ:MIN_DP:PL  0/0:33:93:33:0,93,1395
3   148896156   .   A   <NON_REF>   .   .   END=148896159   GT:DP:GQ:MIN_DP:PL  0/0:36:99:35:0,99,1282
3   148896160   .   G   <NON_REF>   .   .   END=148896160   GT:DP:GQ:MIN_DP:PL  0/0:37:76:37:0,76,1445
3   148896161   .   A   <NON_REF>   .   .   END=148896395   GT:DP:GQ:MIN_DP:PL  0/0:81:99:37:0,107,1356
3   148896396   .   C   G,<NON_REF> 1171.77 .   BaseQRankSum=1.677;DP=61;MLEAC=1,0;MLEAF=0.500,0.00;MQ=60.00;MQRankSum=0.719;ReadPosRankSum=0.849   GT:AD:GQ:PL:SB  0/1:27,34,0:99:1200,0,921,1282,1023,2305:4,23,1,33
3   148896397   .   C   <NON_REF>   .   .   END=148896444   GT:DP:GQ:MIN_DP:PL  0/0:52:99:40:0,105,1575
3   148896445   .   C   <NON_REF>   .   .   END=148896445   GT:DP:GQ:MIN_DP:PL  0/0:40:86:40:0,86,1515
3   148896446   .   C   <NON_REF>   .   .   END=148896447   GT:DP:GQ:MIN_DP:PL  0/0:38:99:38:0,99,1485
3   148896448   .   T   <NON_REF>   .   .   END=148896449   GT:DP:GQ:MIN_DP:PL  0/0:39:90:38:0,90,1350

gVCF file 2:

3   148895575   .   T   <NON_REF>   .   .   END=148895818   GT:DP:GQ:MIN_DP:PL  0/0:126:99:60:0,120,1800
3   148896150   .   A   <NON_REF>   .   .   END=148896150   GT:DP:GQ:MIN_DP:PL  0/0:33:96:33:0,96,1440
3   148896151   .   A   <NON_REF>   .   .   END=148896395   GT:DP:GQ:MIN_DP:PL  0/0:77:99:34:0,99,1485
3   148896396   rs139633388 C   G,<NON_REF> 1035.77 .   BaseQRankSum=0.571;ClippingRankSum=0.313;DB;DP=68;MLEAC=1,0;MLEAF=0.500,0.00;MQ=60.00;MQRankSum=0.608;ReadPosRankSum=-0.006 GT:AD:DP:GQ:PL:SB   0/1:32,36,0:68:99:1064,0,933,1160,1042,2202:8,24,11,25
3   148896397   .   C   <NON_REF>   .   .   END=148896432   GT:DP:GQ:MIN_DP:PL  0/0:55:99:38:0,99,1485
3   148896433   .   A   <NON_REF>   .   .   END=148896434   GT:DP:GQ:MIN_DP:PL  0/0:38:96:38:0,96,1440
3   148896435   .   T   <NON_REF>   .   .   END=148896435   GT:DP:GQ:MIN_DP:PL  0/0:38:99:38:0,99,1485