Defind Files

Defind: detecting genomic deletions by integrating read depth, GC content, mapping quality and paired-end mapping signatures of next generation sequencing data.

Defind is offered as open source software and is licensed under the GNU General Public License version 3 (GPLv3). Thanks for your interest in our works.

Prerequisites:
SAMtools: http://samtools.sourceforge.net
Tabix: http://samtools.sourceforge.net/tabix.shtml
Bcftools: http://samtools.sourceforge.net
R: http://cran.r-project.org/
The R package "IRanges"(http://www.bioconductor.org/packages/2.11/bioc/html/IRanges.html) is also needed by Defind.


INSTALL:
tar xzf Defind.tar.gz
cd Defind
export PERL5LIB=`pwd`/script:$PERL5LIB
export PATH=`pwd`/script:$PATH

Type "Defind.pl" on the command line for detailed parameters of Defind:
Usage:   perl Defind.pl
	-m STR bam_file	[]
	-r STR reference_seq	[]
	-n STR chromosome	[]
	-i INT insert_size_mean	[]
	-d INT insert_size_sd	[]
	-a STR the concensus file has already been created	[yes]
	-s STR samtools_exe_path	[samtools]
	-t STR tabix_exe_path	[tabix]
	-c STR bcftools_exe_path	[bcftools]
	-g STR bgzip_exe_path	[bgzip]
	-R STR R_exec_path	[R]
	-q INT mapping_quality_cutoff_4_PEM_del	[35]
	-x INT max_del_size_detected_by_PEM	[500000]
	-o INT min_read_pair_support_for_PEM_del	[2]
	-z INT left_extend_length_for_DOC_del	[3000]
	-y INT right_extend_length_for_DOC_del	[3000]
	-b INT mapping_quality_cutoff_for_shrinking	[20]
	-u INT mapping_quality_cutoff_for_extending	[40]
	-f INT coverage_cutoff_for_shrinking	[1]
	-p INT coverage_cutoff_for_extending	[4]
	-w INT sliding_window_size_for_extending	[40]
	-k INT sliding_window_size_for_shrinking	[10]
	-e INT score_cutoff_for_PEM_del	[20]


The best way to get familiar with the usage of Defind is to walk through the example dataset. The directory "exam_data" contains two subdirectory: "Input" and "Output". The input files for Defind is in the Input directory and the Output directory contains the pre-calculated results. Go to the Input directory and type "Defind.pl -m chr05_sorted.bam -r chr05.fasta -n chr05 -i 180 -d 20 -a no" to get the result. The final results would be in file: chr05.defind.out. You can compare it with the pre-calculated results in the Output directory.



Wen Yao <ywww@webmail.hzau.edu.cn>