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  • We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov). We used SNPdetector for SNP discovery as part of the HapMap project [7]. To compare the performance of SNPdetector with the other SNP detection programs, we reanalyzed a subset of ENCODE data (61 amplicons on Chromosome 18) using PolyPhred 5.0.2 and NovoSNP [17] (a new SNP detection software package). During the development of SNPdetector, we used the mouse resequencing data as the training dataset because heterozygotes in inbred mouse strains are almost always false positive as a result of mouse breeding history. SNPdetector runs on Unix and Linux and is publicly available by anonymous ftp (http://lpg.nci.nih.gov). SNPdetector was implemented in C and Perl.
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