#Sprites
Written by Zhen Zhang ([email protected])
Jianxin Wang Lab, Central South University
Please cite:
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 the links below:
- Linux 64bit: sprites_Linux64
- OS X: sprites_OSX
##Installation
- HTSlib (http://www.htslib.org/)
- BamTools (https://github.com/pezmaster31/bamtools)
- CMake (http://www.cmake.org)
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