SNPAAMapperT2K



Please cite: Bai, Y. “SNPAAMapperT2K: A genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI.tbl data files”. Bioinformation 10(11). 711-15. 2014.


SNPAAMapperT2K is a genome-wide SNP downstream analysis and annotation pipeline using next-generation sequencing data for Arabidopsis.

It can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5'UTR, etc) for species whose chromosome files are annotated as NCBI .tbl format.

SNPAAMapperT2K algorithm consists of two major modules and custom scripts:



Methodology



Utility

Please dump all files in the same directory on Unix or Mac machines. Also, please make sure that BWA and SAMTools are pre-installed on the path and TAIR genome files need to be BWA indexed first. The user can simply type:
      ./run_SNPAAMapperT2K.sh configT2K.txt



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