GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment
 

I am trying (and failing) to call SNPs using a reference file (.BED) specifically for the Agilent 50Mb Sureselect enrichment sequencing. I am using the GATK UnifiedGenotyper with the following commands. Any ideas? Thanks!

java -jar ~/Sting/dist/GenomeAnalysisTK.jar \
-R ~/Documents/refFASTA/SureSelect_All_Exon_50mb.bed \
-l INFO \
-T UnifiedGenotyper \
-I ~/Documents/next_gen/sorted.N.dupesremoved.recali.bam \
-o ~/Documents/SNP/N_AgilentSS_50MB_gatk.vcf \
-stand_call_conf 50.0 \
-stand_emit_conf 10.0 \
-dcov 150

solved
 

The above code should have contained the argument "-L" for the interval list (bed) file and also a "-R" for the reference fasta file!