                                    BS tools
                       Tools for the analysis of BS-Seq data
                                Version 0.1
                                 May, 2014

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Table of Contents
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  1.   Overview
  3.   Usage
  4.   Contact
  5.   References

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1. Overview
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BS tools are designed for the analysis of BS-Seq data, from bisulfite read 
mapping to SNP and methylation level calling at single-nucleotide resolution.
It consists out of two main tools: Bisar and Casbar.

Bisar reads three-letter mappings of bisulfite reads and computes 
local pairwise four-letter realignments using an advanced statistical 
alignment model.

These alignments can be then used in the subsequent tool Casbar for a simultaneous 
SNP and methylation level calling. A Bayesian model is used to compute the 
posterior probability for each possible genotype under the observed data 
and a given methylation level. The methylation level maximizing the 
posterior probability is determined and the genotype with the highest 
probability is chosen.

The files README.bisar and README.bisar contain detailed documentation of 
the respective tools.

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3. Usage
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The binaries bisar and casbar can be found in the directory "bin".
Each program has a verbose built-in help that you can view using the "--help"
option. For example,

  $ bisar --help
  $ casbar --help

prints the help for the respective tools.

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4. Contact
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For questions or comments, contact:
  Sabrina Krakau <sabrina.krakau@fu-berlin.de>
or
  David Weese <david.weese@fu-berlin.de>

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5. References
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More detailed information you can find in the following document:
http://www.mi.fu-berlin.de/en/inf/groups/abi/theses/master_dipl/krakau/
msc_thesis_krakau.pdf?1394119375

