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



Yongsheng Bai1, 2



1Department of Biology, 2The Center for Genomic Advocacy, Indiana State University 600 Chestnut Street, Terre Haute, IN 47809, U.S.A


Email; *Corresponding author


Article Type




Received November 18, 2014; Accepted November 19, 2014; Published November 27, 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



Bai, Bioinformation 10(11): 711-715 (2014)

Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.