How do I filter the reads that result in this type of error in some of my intervals?

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Only one of refStart or refStop must be < 0, not both (-1, -8)

Here is some information

INFO  20:22:19,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-16-g9f648cb, Compiled 2012/12/04 03:48:10 
INFO  20:22:19,452 HelpFormatter - Program Args: -T HaplotypeCaller

Thanks