Running GATK HaplotypeCaller over just one chromosome of a whole genome bam file

Question

[michael.flower.14]

I'm only interested in variants on chromosome 4, so to speed things up I'd like to run HaplotypeCaller on just chromosome 4. I'm trying with this:

gatk HaplotypeCaller -R $REF -I "$BAM" -O "$DIR"/gatk/$PREFIX"_hg19_chr4_HaplotypeCallerPGT.vcf" -ERC GVCF -L chr4

But I get an error saying there's no positional argument. I'm not sure what it means or how to resolve! I've tried reading around, and can't see a solution.

***********************************************************************

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',/Volumes/Seagate Expansion Drive/temp/125QiPSC_rg.bam}' but no positional argument is defined for this tool.

***********************************************************************

[michael.flower.14]

I resolved it, I just hadn't defined $REF. Sorry!