I have a VCF file with this line (i.e. GT=0/1=G/T):
20 10120854 . G T,A 32175.56 . AC=399,18;AF=0.111,5.006e-03;AN=3596;BaseQRankSum=1
.03;DP=6710;FS=2.485;GQ_MEAN=15.45;GQ_STDDEV=20.21;InbreedingCoeff=0.1235;MLEAC=416,17;MLEAF=0.116,4.727e-03;MQ=60.00;MQ0=0
;MQRankSum=0.358;NCC=189;QD=18.08;ReadPosRankSum=0.358 GT:AD:DP:GQ:PL 0/1:1,3,0:.:34:123,0,34,126,43,169
When I run it through version 3.2 of LeftAlignAndTrimVariants with the --splitMultiallelics flag, then the genotype information is lost; i.e. GT=./. and the output is:
20 10120854 . G T 32175.56 . BaseQRankSum=1.03;DP=6710;FS=2.485;GQ_MEAN=15.45;GQ_STDDEV=20.21;InbreedingCoeff=0.1235;MLEAC=416,17;MLEAF=0.116,4.727e-03;MQ=60.00;MQ0=0;MQRankSum=0.358;NCC=189;QD=18.08;ReadPosRankSum=0.358 GT ./.
20 10120854 . G A 32175.56 . BaseQRankSum=1.03;DP=6710;FS=2.485;GQ_MEAN=15.45;GQ_STDDEV=20.21;InbreedingCoeff=0.1235;MLEAC=416,17;MLEAF=0.116,4.727e-03;MQ=60.00;MQ0=0;MQRankSum=0.358;NCC=189;QD=18.08;ReadPosRankSum=0.358 GT ./.
I have attached the input VCF. I also got rid of the PL information, but still got the unexpected output.
Maybe I should just write some code for normalizing variants myself in order to save time 
Thank you very much as always!