README
________________________________________________________________________

These perl scripts are associated with the manuscript "A streamlined method 
for detecting structural variants in cancer genomes by short read paired-end 
sequencing". Please find brief descriptions, usage information and module
requirements below.
________________________________________________________________________

PE.pl

PE.pl is a script that simulates paired end sequencing data and writes 
fastq files in the Illumina format. It selects random positions in the 
user-provided genome, normalized for different chromosome lengths. 
User-defined parameters include the number of read pairs, read length, 
mean insert size and standard deviation.

Requirements: 
Math::Random

Usage: 
perl PE.pl <seq_files_extension> <number_of_readpairs> <readlength> <mean_insert_size> <st_deviation> <output_file_prefix> 

________________________________________________________________________

links.pl

links.pl takes the SVDetect (http://svdetect.sourceforge.net) "linking"
output file (*.links) as input, searches for "imperfect duplicates" (reads 
with 1-2 bp offset in coordinates) and outputs a modified *.links file
with imperfect duplicates removed.

The script requires three arguments: (1) The read length, (2) the input 
filename, and (3) the output filename. 

________________________________________________________________________

Preprocess_rm0to22.pl
Preprocess_rm_normal.pl

Preprocess_rm0to22.pl and Preprocess_rm_normal.pl are scripts that modify
BWA sam files. Preprocess_rm0to22.pl removes all read pairs where one or 
both reads in a pair have mapping qualities 0-22. Preprocess_rm_normal.pl
removes concordant read pairs.

Usage:   
Preprocess_rm_normal.pl <file.sam>
Output file with extension .rm_normal.sam is produced.

Preprocess_rm0to22.pl <file.sam>
Output file with extension .rm0to22.sam is produced.