Using GATK to call SNPs in RNA-seq data

[zorph]

has anyone ever used SNP calling from RNA-seq data?
I am currently trying to do this but GATK is calling the reference as the variant??? I have checked my reference file and it's perfectly correct.

I don't know if this a result from me using RNA-seq or just my command.

I am using an older version of gatk because it doesn't require the extensive file modifications that is required of the newer versions.

My command is below:

GenomeAnalysisTK.jar
-T UnifiedGenotyper
-l INFO
-I file.bam
-R Homo_sapiens_assembly18.fasta
-U ALLOW_UNINDEXED_BAM
--assume_single_sample_reads sample_name
--platform SOLEXA
-dcov 300
-varout file.vcf
-nt 1
-bad_mates

any advice?