Genome-wide DNA polymorphism analyses using VariScan

Background: DNA sequence polymorphisms analysis can provide
valuable information on the evolutionary forces shaping nucleotide
variation, and provides an insight into the functional significance
of genomic regions. The recent ongoing genome projects will
radically improve our capabilities to detect specific genomic
regions shaped by natural selection. Current available methods and
software, however, are unsatisfactory for such genome-wide
analysis. Results: We have developed methods for the analysis of
DNA sequence polymorphisms at the genome-wide scale. These methods,
which have been tested on a coalescent-simulated and actual data
files from mouse and human, have been implemented in the VariScan
software package version 2.0. Additionally, we have also
incorporated a graphical-user interface. The main features of this
software are: i) exhaustive population-genetic analyses including
those based on the coalescent theory; ii) analysis adapted to the
shallow data generated by the high-throughput genome projects; iii)
use of genome annotations to conduct a comprehensive analyses
separately for different functional regions; iv) identification of
relevant genomic regions by the sliding-window and
wavelet-multiresolution approaches; v) visualization of the results
integrated with current genome annotations in commonly available
genome browsers. Conclusion: VariScan is a powerful and flexible
suite of software for the analysis of DNA polymorphisms. The
current version implements new algorithms, methods, and
capabilities, providing an important tool for an exhaustive
exploratory analysis of genome-wide DNA polymorphism data.