targetDepth Version 1.0.0

Copyright Alex M. Mawla 2015. All Rights Reserved.

Takes in an indexed coverage file with a partition csv file identifying regions of interest, and outputs depth of coverage files for each partition of interest.

Requirements: Samtools (http://samtools.sourceforge.net). Samtools binary must be located in /usr/bin or specified in the terminal shell environment path.

Input:

1. Indexed Coverage file (BAM format) [required]

2. Partition file (CSV format) [required] Four columns:
   Partition Name, Chromosome, Start Position, Stop Position

3. Reference genome (bed format) [required]

4. Output directory [optional]