SNPdetector: a software tool for sensitive and accurate SNP detection

摘要: Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery genetic predisposition to complex diseases. PCR resequencing method choice de novo SNP discovery. However, manual curation putative SNPs has been a major bottleneck in application this high-throughput screening. Therefore it critical develop more sensitive accurate computational automated detection. We developed software tool, SNPdetector, identification fluorescence-based reads. SNPdetector was designed model process human visual inspection very low false positive negative rate. demonstrate superior performance mutation analysis by comparing its results with those derived inspection, PolyPhred (a popular detection tool), independent genotype assays three large-scale investigations. The first study identified validated inter- intra-subspecies variations 4,650 traces 25 inbred mouse strains that belong either Mus musculus species or M. spretus species. Unexpected heterozgyosity CAST/Ei strain observed two out 1,167 SNPs. second 11,241 candidate five ENCODE regions genome covering 2.5 Mb genomic sequence. Approximately 50% were selected experimental genotyping; validation rate exceeded 95%. third detected ENU-induced (at 0.04% allele frequency) 64,896 1,236 zebra fish. Our large diverse test datasets demonstrated an effective tool genome-scale research large-sample clinical studies. runs on Unix/Linux platform available publicly (http://lpg.nci.nih.gov).