Calling invaiant sites with the new pipeline of HaplotypeCaller

Hello,

I am using the new pipeline of haplotype caller in order to obtain a vcf file containing both variant and invariant sites.

For each individual, I called variant and invariant sites :

java -Xmx300g -jar GenomeAnalysisTK.jar \
     -T HaplotypeCaller \
     -R ref.fasta \
     -I ${INPUT}.bam \
     --genotyping_mode DISCOVERY 
     -stand_emit_conf 0 \
     -stand_call_conf 0 \
     -o ${INPUT}\_VC.vcf \
     --emitRefConfidence BP_RESOLUTION  \
     --variant_index_type LINEAR \
     --variant_index_parameter 128000 \
     -nct 16

In the vcf that I obtain, I indeed have every position.
The problem is that he INFO and QUAL fileds are empty (.) if the site is non variant.

KE332545.1      44      .       T       <NON_REF>       .       .       .       GT:AD:DP:GQ:PL  0/0:13,0:13:39:0,39,503
KE332545.1      45      .       T       <NON_REF>       .       .       .       GT:AD:DP:GQ:PL  0/0:13,0:13:39:0,39,518
KE332545.1      46      .       C       T,<NON_REF>     0       .       BaseQRankSum=-2.270;ClippingRankSum=-0.691;DP=17;MLEAC=0,0;MLEAF=0.00,0.00;MQ=38.98;MQ0=0;MQRankSum=0.099;ReadPosRankSum=0.493  GT:AD:DP:GQ:PL:SB      0/0:11,2,0:13:3:0,3,379,33,385,414:0,0,0,0
KE332545.1      47      .       C       <NON_REF>       .       .       .       GT:AD:DP:GQ:PL  0/0:13,0:13:39:0,39,515
KE332545.1      48      .       A       <NON_REF>       .       .       .       GT:AD:DP:GQ:PL  0/0:13,0:13:39:0,39,540
KE332545.1      49      .       C       <NON_REF>       .       .       .       GT:AD:DP:GQ:PL  0/0:13,0:13:39:0,39,563

But I also wanted this information in order to use my filtering pipeline on those invariant sites as well !
Any solution ?

Thanks !

Muriel