Bai Yongsheng
Department of Biology ; The Center for Genomic Advocacy, Indiana State University 600 Chestnut Street, Terre Haute, IN 47809, U.S.A.
Bioinformation. 2014 Nov 27;10(11):711-5. doi: 10.6026/97320630010711. eCollection 2014.
SNPAAMapper, a genome-wide SNP downstream analysis and annotation pipeline, was designed to classify detected variants according to genomic regions and report the mutation class by processing whole-genome and/or whole-exome sequencing data. A widely used sequence and data annotation table format "knownGene.txt" has not yet been created for many popular model organisms (e.g. Arabidopsis). Instead, NCBI .tbl annotation format files are provided for these species. Therefore, it is of interest to describe SNPAAMapperT2K, a genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI .tbl data files (e.g. Arabidopsis). The pipeline is tested with a deeply sequenced Arabidopsis thaliana strain (Seattle-0). The SNPAAMapperT2K can also annotate and report SNP classes for other species, whose chromosome files are annotated as NCBI .tbl format, but do not have their annotated knownGene.txt files available.
Perl scripts and required input files are available on the web at http://isu.indstate.edu/ybai2/SNPAAMapperT2K.
SNPAAMapper是一个全基因组SNP下游分析和注释流程，旨在根据基因组区域对检测到的变异进行分类，并通过处理全基因组和/或全外显子组测序数据来报告突变类别。许多常用模式生物（如拟南芥）尚未创建广泛使用的序列和数据注释表格式“knownGene.txt”。相反，这些物种提供的是NCBI.tbl注释格式文件。因此，描述SNPAAMapperT2K很有意义，它是一个用于对用NCBI.tbl数据文件注释的物种（如拟南芥）进行全基因组SNP下游分析和注释的流程。该流程已在深度测序的拟南芥品系（西雅图-0）上进行了测试。SNPAAMapperT2K还可以为其他物种注释和报告SNP类别，这些物种的染色体文件注释为NCBI.tbl格式，但没有可用的注释knownGene.txt文件。
Perl脚本和所需输入文件可在网页http://isu.indstate.edu/ybai2/SNPAAMapperT2K上获取。
