#Sprites

Written by Zhen Zhang (zhangz@csu.edu.cn)
Jianxin Wang Lab, Central South University

Please cite:

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Current version: 0.3.0

Support for Linux and OS X

##Summary Sprites is a sv caller that specializes in detecting deletion from low-coverage sequencing data. It works by identifying split reads from alignments based on soft-clipping information. By re-aligning a split read to one of its target sequences derived from paired-end reads that span it, a deletion is predicted and breakpoint ends are pinpointed with base-pair resolution. Sprites uses alignments produced by BWA. Of course, it can also use those produced by other read aligners that support 5'- or 3'-end soft-clipping, like Bowtie2. It can also be extended to detect other types of sv.

##Pre-built binaries You can download the pre-built binaries from the Releases page or use the links below:

• Linux 64bit: sprites_Linux64
• OS X: sprites_OSX

##Installation

Requirements

• HTSlib (http://www.htslib.org/)
• BamTools (https://github.com/pezmaster31/bamtools)
• CMake (http://www.cmake.org)

Building Sprites

git clone https://github.com/zhangzhen/sprites.git
cd sprites
export BAMTOOLS_HOME=/path/to/bamtools
export HTSLIB_HOME=/path/to/htslib
mkdir build
cd build
cmake ..
make
cp sprites /usr/local/bin/

##Usage

sprites [options] sample.bam

The input bam file is required to be sorted.

Options

-r FILE