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:
-
Indexed Coverage file (BAM format) [required]
-
Partition file (CSV format) [required] Four columns:
Partition Name, Chromosome, Start Position, Stop Position -
Reference genome (bed format) [required]
-
Output directory [optional]