skip chromosomes GATK HaplotypeCaller

I am trying to use GATK HaplotypeCaller to identify variants on a set of bam files.
however, my bam files contain only data on chrX, but the headers have the @SQ tag for all chromosomes, including the various _gl000etcetc.
so when I run the tool with

java -jar /GATK/v3.6/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R broad_genome/hg19_broad.fasta \
-I myBam.bam \
--genotyping_mode DISCOVERY \
-stand_emit_conf 10 \
-stand_call_conf 30 \
-o ../calls/myBam.vcf

I get the following error:

ERROR MESSAGE: Badly formed genome location: Contig chr1_gl000191_random given as location, but this contig isn't present in the Fasta sequence dictionary

...so, can I tell GATK to ignore all chr BUT chrX?

thank you