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