Replace UnifiedGenotyper with HaplotypeCaller

I have been trying to genotype a list of given positions from BAMs files.
Until today I used UnifiedGenotyper

This was my command and it works fantastic:

FOR %%i IN (*.bam) DO java -jar "GenomeAnalysisTK.jar" -T UnifiedGenotyper -U ALLOW_SEQ_DICT_INCOMPATIBILITY -R "genome.fa" -I %%i -o %%i.redesign.v2.vcf --downsampling_type NONE --genotyping_mode GENOTYPE_GIVEN_ALLELES --alleles Norm.RC.v3.sort.vcf.gz --output_mode EMIT_ALL_SITES -L Norm.RC.v3.sort.vcf.gz

I am trying to move to HaplotypeCaller (because of the local alignment)
I understand I can not use EMIT_ALL_SITES and use HaplotypeCaller with --emitRefConfidence GVCF followed by GenotypeGVCFs

These are my commands:

FOR %%i IN (*.bam) DO java -jar "GenomeAnalysisTk.jar" -T HaplotypeCaller -R "genome.fa" -I %%i --emitRefConfidence GVCF -o %%i.g.vcf --alleles Norm.RC.v3.sort.vcf.gz -L Norm.RC.v3.sort.vcf.gz

FOR %%i IN (*.g.vcf) DO java -jar "GenomeAnalysisTk.jar" -T GenotypeGVCFs -R "genome.fa" --variant %%i -allSites -o %%i.Site_VCF.vcf

At the end of this process, I get additional positions in the Site_VCF.vcf file and the REF ALT for all the positions are not as in the input.vcf file.
Can you explain how this can be resolved?

In addition, I don't get Site_VCF.vcf file the GQ score.

I am using v3.7-0-gcfedb67