In order to measure specificity, we can designate certain partitions as the tumor and others as the normal and process them through MuTect (or any other method). Somatic mutations identified in this process are false positives as they are either germline events that are under-called in the normal, or erroneous variants due to sequencing noise over-called in the partitions designated as tumor. We chose to draw reads from libraries Solexa-18483 and Solexa-23661 for the tumor and from library Solexa-18484 for the normal.
