SNPAAMapperT2K: A genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI.tbl data files

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. AVAILABILITY: Perl scripts and required input files are available on the web at http://isu.indstate.edu/ybai2/SNPAAMapperT2K