spleet

Validate SV with Split-Reads

Install

Clone from GitHub

git clone --recursive https://github.com/dantaki/spleet.git

Compile with CMake

cd spleet/ && mkdir build && cd build && cmake .. && make

Binary executable found under spleet/build/src/spleet

Usage

Spleet currently supports validation of deletion and duplication SV

spleet --help

eeeee   eeeee   e         eeee   eeee   eeeee
8   "   8   8   8         8      8        8
8eeee   8eee8   8e        8eee   8eee     8e
   88   88      88        88     88       88
8ee88   88      88eee     88ee   88ee     88

spleet         Validate SV with Split-Reads
Version: 1.0	Author: Danny Antaki <dantaki@ucsd.edu>

Usage: spleet -i <in.bam> -r <sv.bed> -x <FLOAT> -q <INT> -o <output.txt>

Options:
    -i        Input: BAM filename
    -r        Input: SV bed file
    -x        Minimum reciprocal overlap [0.5]
    -q        Mapping quality threshold [10]
    -o        Output: filename

Input

• -i Input: BAM filename

  • BAM file must be indexed with samtools index

• -r Input: SV bed file

  • The first four tab-delimited columns must be CHROM START END [DEL|DUP]

Output

CHR	START	END	LENGTH	OVERLAP	READNAME	ALIGNMENT	STRANDS	SV	TYPE
22	582	777	196	0.999992	SPLEET-READ	PRIMARY	+|+	22:581-776	DEL

Acknowledgements

spleet uses BamTools

BamTools Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg

Notice: BamTools requires zlib.

License

MIT License

Copyright (c) 2017 Danny Antaki

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Contact

dantaki@ucsd.edu