Full online documentation at:
https://wiki-bsse.ethz.ch/display/ShoRAH/Documentation

ShoRAH consists of several programs:

shorah.py    - runs the following programs
dec.py       - local error correction based on diri_sampler
diri_sampler - Gibbs sampling for Dirichlet process mixture
contain.cc   - eliminate redundant reads
mm.py        - maximum matching haplotype construction
freqEst.cc   - EM algorithm for haplotype frequency
fas2read.pl  - translates between two formats for read data files
bam2msa.py   - extracts a multiple sequence alignment from a BAM file
snv.py       - extracts SNVs from locally reconstructed windows
b2w.c        - creates windows from a bam alignment file
fil.c        - performs a strand bias test on predicted SNVs

Copyright 2007, 2008, 2009, 2010, 2012
Niko Beerenwinkel,
Arnab Bhattacharya,
Nicholas Eriksson,
Moritz Gerstung,
Lukas Geyrhofer,
Osvaldo Zagordi,
Kerensa McElroy,
ETH Zurich
under GPL. See file LICENSE for details.
The program also includes other software written by third parties.
This has been distributed according to the licenses provided by the
respective authors.


GENERAL USAGE:
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Install:
	From within the samtools directory, type 'make'. Then, from within
        shorah directory, type 'make' to build the C++ and C programs, then 
        run. See INSTALL for additional information.

Run:
	Type shorah.py -h for command line instructions. 
        If shorah is run within a directory in which it has already been 
        run, only SNV calling will be performed. This facilitates 
        experimenting with different values of sigma for the strand bias 
        test.

SHORAH.PY:
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Options:
  -h, --help            show this help message and exit
  -b B, --bam=B         sorted bam format alignment file.
  -f F, --fasta=F       reference genome in fasta format.
  -a A, --alpha=A       alpha in dpm sampling <0.01>
  -w W, --windowsize=W  window size <201>
  -s S, --winshifts=S   number of window shifts <3>
  -i I, --sigma=I       value of sigma to use when calling SNVs
  -x X, --maxcov=X      approximate maximum coverage allowed
  -r R, --region=R      region in format 'chr:start-stop', eg 'ch3:1000-3000'
  -k, --keep_files      keep intermediate files (Gibbs sampling)