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SNPs Call using HaplotypeCaller

I am using the following script to call-variants from RNAseq data using HaplotypeCaller. However, in the VCF output I only have 0/1 and 1/1 genotype and there is no 0/0 genotype. How I can get all 3 class of genotype in the output? please advise. Thanks

java -jar /home/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar \
-R /home/ucsc.hg19/ucsc.hg19.fasta \
-T HaplotypeCaller \
-I /home/sample1.bam \
-recoverDanglingHeads \
-dontUseSoftClippedBases \
-stand_call_conf 20.0 -stand_emit_conf 20.0 \
--dbsnp /home/dbsnp_137.hg19.vcf \
--output_mode EMIT_ALL_SITES \
--genotyping_mode DISCOVERY \
--out /home/output.vcf



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