Dependencies:

1. Perl models: Getopt::Long, Time::Local, and Cwd. Installation steps:
>cpan
cpan>install Getopt::Long
cpan>install Time::Local
cpan>install Cwd

2. Samtools version >1.3. 
Mac:
>brew install samtools
Centos:
>sudo yum install samtools
Ubuntu:
>sudo apt-get install samtools

3. Bowtie2.
Mac:
>brew install bowtie2
Centos:
>sudo yum install bowtie2
Ubuntu:
>sudo apt-get install bowtie2

4. VarScan. See installation instruction in VarScan website. 

5. R base and Bioconductor package “ggbio” (optional). See installation instruction in R website. 

Required files:
1.	Input data files (fastq format).
2.	Reference genome (fasta format). 
3.	Gene annotation file (GTF format). 

Example commad:
perl BSREx.pl --b_fqp_wt=wt_1.fastq wt_2.fastq --b_fqp_mu=mu_1.fastq mu_2.fastq --reference=maize.3_4.ref.fa --gtf=GRMZM2G139797.gtf --threads=10 --output=test



