GenotypeGVCF INFO field empty

Hello GATK,

I am trying to run VQSR on a set of 50 samples. I ran the following haplotypeCaller command:
$JAVA -Xmx30g -XX:ParallelGCThreads=1 -Djava.io.tmpdir=/tmp -jar $GATK -T HaplotypeCaller -R $REF -I $BAM -stand_call_conf 30.0 -stand_emit_conf 10.0 -A MappingQualityRankSumTest -A AlleleBalance -A BaseCounts -A ChromosomeCounts -A QualByDepth -A ReadPosRankSumTest -A HaplotypeScore -A LowMQ -A RMSMappingQuality -A BaseQualityRankSumTest -A VariantType -A Coverage -A GCContent -A HomopolymerRun -A InbreedingCoeff -A FisherStrand -A ChromosomeCounts -D $DBSNP -nct 4 -rf BadCigar --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o $TEMP/${PREFIX}.$J.hc.g.vcf -et NO_ET

and then the GenotypeGVCFs command as:
/projects/sw/jdk1.7.0_03/bin/java -jar /projects/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T GenotypeGVCFs -R /projects/Genomes/fasta/Human_GRC_build37_1kGproject/human_g1k_v37_Ensembl_MT_66.fasta -V /scratch/SC/analysis-vqsr/ENRID31/hc/gvcf_list_ENRID31.list -A StrandOddsRatio -A QualByDepth -A FisherStrand -A MappingQualityRankSumTest -A ReadPosRankSumTest -A RMSMappingQuality -A BaseQualityRankSumTest -o /scratch/SC/analysis-vqsr/ENRID31/hc/output_gvcfs.vcf --dbsnp /projects/GATK_resourceBundle/ftp.broadinstitute.org/bundle/2.8/b37/dbsnp_138.b37.vcf -stand_call_conf 30.0 -stand_emit_conf 10.0 -L /projects/ENRID31/ENRID31.bed

The problem is that the INFO field is empty. For both the intermediate gvcf files , the output is like
1 10015 . A . . . GT:DP:GQ:MIN_DP:PL 0/0:3:0:3:0,0,29
1 10016 . C . . . GT:DP:GQ:MIN_DP:PL 0/0:3:3:3:0,3,45
1 10021 . A . . . GT:DP:GQ:MIN_DP:PL 0/0:3:0:3:0,0,36
1 10022 . C . . . GT:DP:GQ:MIN_DP:PL 0/0:3:3:3:0,3,45
1 10027 . A . . . GT:DP:GQ:MIN_DP:PL 0/0:3:0:3:0,0,0
1 10028 . C . . . GT:DP:GQ:MIN_DP:PL 0/0:3:3:3:0,3,45
1 10033 . A . . . GT:DP:GQ:MIN_DP:PL 0/0:3:0:3:0,0,0
1 10034 . C . . . GT:DP:GQ:MIN_DP:PL 0/0:5:3:3:0,3,45
1 10039 . A . . . GT:DP:GQ:MIN_DP:PL 0/0:5:0:5:0,0,7
1 10040 . C . . . GT:DP:GQ:MIN_DP:PL 0/0:5:3:5:0,3,45

and the output vcf file as,

1 14671 rs201055865 G C 2156.44 . DB;FS=0.000;MLEAC=2;MLEAF=0.500;QD=3.29 GT:AD:GQ:PL ./. ./. 0/1:289,86:99:1436,0,8216 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:225,55:99:749,0,5926 ./. ./. ./. ./. ./. ./. ./.
1 14673 rs369473859 G C 710.01 . DB;DP=625;FS=53.168;MLEAC=4;MLEAF=0.182;QD=1.54 GT:AD:DP:GQ:PL 0/1:93,19:.:99:193,0,2465 0/1:98,15:.:76:76,0,3208 ./. ./. ./. ./. ./. 0/1:98,24:.:99:331,0,2463 ./. 0/0:224,0:224:67:0,67,6707 0/1:97,18:.:99:159,0,3167 ./. 0/0:223,0:223:64:0,64,6787 ./. 0/0:149,13:.:99:0,115,4968 0/0:104,8:.:99:0,107,3267 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:112,9:.:99:0,122,3811 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:178,0:178:0:0,0,4936 ./. ./. ./. ./. ./. ./. 0/0:179,18:.:59:0,59,4832 ./. ./. ./.
1 14677 rs201327123 G A 10743.90 . DB;FS=8.169;MLEAC=16;MLEAF=0.471;QD=2.95 GT:AD:GQ:PL ./. 0/1:72,39:99:702,0,2037 ./. ./. ./. ./. ./. ./. ./. 0/1:179,49:99:697,0,4943 0/1:80,42:99:806,0,2321 ./. ./. ./. 0/1:121,45:99:1194,0,4495 0/1:82,31:99:520,0,2190 ./. ./. 0/1:205,34:99:216,0,5652 0/1:169,46:99:616,0,4411 ./. ./. ./. ./. ./. ./. 0/1:77,45:99:900,0,2102 ./. ./. ./. ./. 0/1:409,85:99:905,0,15955 ./. ./. 0/1:315,40:51:51,0,8506 0/1:210,33:99:155,0,7484 0/1:210,33:99:157,0,7371 ./. ./. 0/1:131,38:99:567,0,3564 0/1:112,57:99:1072,0,2854 ./. ./. ./. 0/1:165,31:99:278,0,4464 ./. ./. 0/1:331,123:99:1977,0,11777 0/0:453,57:33:0,33,16260 ./.

All the other annotations mentioned in the commands like MappingQualityRankSumTest, ReadPosRankSumTest etc cannot be seen in any of the outputs !!!
I am new to GATK and don't really understand where I may be going wrong.. Any help is appreciated..

Thanks

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