Haplotype caller 3.2 versions not calling a true variant

[Grebmot]

Hi! I have just run the 3.2.2 and 3.2.0 versions on the same bam file and I noticed that it is not calling a true variant, while the earlier version 3.1.1 calls it. Everything in the command is identical aside from GATK haplotype caller version. Any ideas why this variant is not called and how to address that? (it's the middle variant chr10:43022236)
Thanks for all the ideas!

##GATKCommandLine=<ID=HaplotypeCaller,Version=3.1-1-g07a4bf8,Date="Mon Aug 25 15:45:14 EDT
10 42823862 . C T 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.568;ClippingRankSum=-0.633;DP=11;FS=8.751;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-1.036;QD=11.43;ReadPosRankSum=0.000 GT:ADP:GQ:PL 0/1:4,6:10:99:154,0,121
10 43022236 . A C 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.368;ClippingRankSum=0.421;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.421;QD=14.97;ReadPosRankSum=-0.421 GT:ADP:GQ:PL 0/1:4,4:8:99:148,0,129
10 43159396 . G A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88 GT:ADP:GQ:PL 1/1:0,2:2:6:49,6,0


##GATKCommandLine=<ID=HaplotypeCaller,Version=3.2-0-g289df4b,Date="Mon Aug 25 15:46:43 EDT
10 42823862 . C T 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.568;ClippingRankSum=-1.036;DP=11;FS=8.751;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=0.000;QD=10.80;ReadPosRankSum=0.365 GT:ADP:GQ:PL 0/1:4,6:10:99:147,0,124
10 43159396 . G A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88 GT:ADP:GQ:PL 1/1:0,2:2:6:49,6,0


##GATKCommandLine=<ID=HaplotypeCaller,Version=3.2-2-gec30cee,Date="Mon Aug 25 13:43:53 EDT
10 42823862 . C T 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.568;ClippingRankSum=-0.365;DP=11;FS=8.751;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-0.741;QD=10.80;ReadPosRankSum=0.365 GT:ADP:GQ:PL 0/1:4,6:10:99:147,0,124
10 43159396 . G A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88 GT:ADP:GQ:PL 1/1:0,2:2:6:49,6,0