N.B. This is a fork of the original work done by Giuseppe Narzisi. Fixes include:
- Replace loading of full genome into memory by runtime extraction of sequence from an indexed genome via ```samtools faidx```
- Fix bug in Microassembler.hh
- Added FORMAT and sample fields to vcf. Added proper header fields
- Somatic assignment more liberal (sufficient for genotype to be different 
between normal and tumor, i.e. ALT can be non-zero for normal as long as it's 
different from the tumor ALT assignment)

Introduction
============

What is Scalpel?
----------------

Scalpel is a DNA micro-assembly pipeline for detecting 
INDEL (INsertion and DEletion) mutations in Next-Generation Sequencing (NGS) data.

What does it mean that Scalpel is in "beta"?
--------------------------------------------

Scalpel is currently under active development and it will be likely to see
changes in the output and command line parameters in the near future.

Obtaining Scalpel
=================

Scalpel can be downloaded from the Sourceforge site at the following address:

http://sourceforge.net/projects/scalpel/

The package has been tested under Linux and Mac OS X operating systems.

Building from source
--------------------

Building and running Scalpel from source requires a GNU-like environment with 

1. GCC
2. GNU Make
3. GNU CMake
4. Perl 5.10 or later

It should be possible to build Scalpel on most Linux installations 
or on a Mac installation with [Xcode and Xcode command line tools] installed.

Instructions to install Xcode (Mac only): 
(1) install Xcode
(2) open XCode -> Preferences -> Downloads -> Download XCode Command Line Tools [needed for 'make']

First, download the source package from the sourceforge site. 
Unzip the file, change to the unzipped directory, and build the
scalpel by running GNU `make` (usually with the command `make`, but
sometimes with `gmake`) with no arguments.  

Adding to PATH
--------------

By adding your Scalpel directory to your PATH (environment variable), you
ensure that whenever you run `scalpel` from the command line, you will get 
the version you just installed without having to specify the entire path.  
This is recommended for most users.  To do this, follow your operating system's 
instructions for adding the directory to your PATH.

Memory requirements
-------------------

For the human genome, a minimum of 3GB of RAM is required to run Scalpel. 
However, a machine with 10GB of RAM is recommended.

Documentation
=============

See included file MANUAL for details.

Wrapper
-------

The `scalpel` executable is actually a Perl wrapper script that orchestrates 
the pipeline analysis. It is recommended that you always run the `scalpel` directly.

License
=======

Scalpel is released under the MIT License.
Copyright (c) 2013-2014 Giuseppe Narzisi and Michael C. Schatz

See included file LICENSE for details.

Contact
======

If you have questions, comments, suggestions, bug reports, etc.
please send them to:

Giuseppe Narzisi 
Cold Spring Harbor Laboratory
Email: gnarzisi@cshl.edu
Project Website: http://sourceforge.net/projects/scalpel/