Variant calling without matched normal sample
If you just want to filter out calls present in dbSNP then use:

java -jar GenomeAnalysisTK.jar \
   -T SelectVariants \
   -R reference.fasta \
   -V patient.vcf \
   --discordance dbSNP.vcf \
   -o patient.filtered.vcf


--discordance will produce calls not present in dbSNP.