ava.lang.OutOfMemoryError: GC overhead limit exceeded

##### ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: An error occurred during the traversal.  Message=GC overhead limit exceeded

问题产生原因：

根据sun的说法： "if too much time is being spent in garbage collection: if more than 98% of the total time is spent in garbage collection and less than 2% of the heap is recovered, an OutOfMemoryError will be thrown."

jvm gc行为中超过98%以上的时间去释放小于2%的堆空间时会报这个错误。

处理方法：

1. 在jvm启动参数中添加 "-XX:-UseGCOverheadLimit"，该参数在JDK6中默认启用("-XX:+UseGCOverheadLimit")。

　　调整后的生产环境中使用的参数为：　　　

JAVA_OPTS='-Xms512m -Xmx4096m -XX:MaxPermSize=128m -XX:-UseGCOverheadLimit -XX:+UseConcMarkSweepGC'