GATK : Drop in number of confidently called bases

[claratsm]

We called the SNPs using GATK v1.0.5506 before and decided to recall using the recent version v1.2-4; however, we found a dramatical decrease in number of confidently called bases from ~90 to ~20%.

Can anyone suggest what's the problem?

Here is the old command and summary (taking a small region as an example),

--------------------------------------------------------------------------------------
java -Xmx4g -jar GenomeAnalysisTK-1.2-4-gd9ea764/GenomeAnalysisTK.jar \
-I recalibrated.bam \
-T UnifiedGenotyper \
-l INFO \
-R human_g1k_v37.fa \
--dbsnp dbsnp_132.b37.vcf \
-o test.raw.SNP.vcf \
-metrics test.raw.SNP.variants \
-glm SNP \
-stand_call_conf 50 \
-stand_emit_conf 10 \
-dcov 500 \
-nt 1 \
-L 11:76260000-76270000 \
-S LENIENT

================================
Visited bases 10001
Callable bases 9992
Confidently called bases 152
% callable bases of all loci 99.910
% confidently called bases of all loci 1.520
% confidently called bases of callable loci 1.521
Actual calls made 5
--------------------------------------------------------------------------------------
And the new command
java -Xmx4g -jar GenomeAnalysisTK-1.0.5506/GenomeAnalysisTK.jar \
-I recalibrated.bam \
-T UnifiedGenotyper \
-l INFO \
-R human_g1k_v37.fa
-B:dbsnp,vcf dbsnp_132.b37.vcf \
-o test.oldUG.raw.SNP.vcf \
-metrics test.oldUG.variants \
-glm SNP \
-stand_call_conf 50 \
-stand_emit_conf 10 \
-dcov 500 \
-nt 1 \
-L 11:76260000-76270000 \
-S LENIENT

==================================
Visited bases 10001
Callable bases 9990
Confidently called bases 9988
% callable bases of all loci 99.890
% confidently called bases of all loci 99.870
% confidently called bases of callable loci 99.980
Actual calls made 5