Consequences of SomaticScore filtering in GT versus CT analysis. A: Number of variants identified in GT (black bars) and CT (grey bars) analyses passing a certain SomaticScore filter, respectively. More variants meeting stringent filtering criteria are identified in the CT analysis. In addition, the ratio of the number of variants in CT to GT analysis is provided inside the graph. B: Some characteristics of the variants identified in GT and CT analyses, respectively. Even though a higher number of variants is found in the GT analysis, a lower number passes the SomaticScore filter of 0.5, as compared to the CT analysis. Among these are only a few SNPs (which are the most reliable called variants), all of which have records in dbSNP. In contrast, all variants identified in the CT analysis, represent SNPs and all of them, but one, have not been reported before.
Nickles et al. BMC Genomics 2012 13:477 doi:10.1186/1471-2164-13-477