Coverage_Mapping

Basic Usage

The Coverage_Mapping handler generates text-based histograms using the BEDTools' coverage or genomecov tools. This script accepts a list of BAM files as its input and will generate a histogram for each BAM file specified. Summary statistics such as the average coverage, median coverage, and maximum coverage are also calculated. Plotted histograms using R are under development for future release.

To run Coverage_Mapping, all common variables and handler-specific variables must be defined within the configuration file. Once the variables have been defined, Coverage_Mapping can be submitted to a job scheduler with the following command (assuming that you are in the directory containing sequence_handling):

./sequence_handling Coverage_Mapping Config

Where Config is the full file path to the configuration file.

Handler-Specific Variables

The following are a list of variables that need to be defined within Config. In addition to the handler-specific variables, all common variables must be defined.

Variable	Function
CM_QSUB	QSub settings for batch submission. Recommended settings are "mem=22gb,nodes=1:ppn=16,walltime=24:00:00".
BAM_LIST	A list of full file paths to the finished BAM files. This can be generated with sample_list_generator.sh.
REGIONS_FILE	A list of regions over which coverage should be calculated, in BED format, specific to the reference genome that was used in Read_Mapping. This is used for exome capture data. For whole-genome sequencing, leave this variable blank.

Output

Coverage_Mapping generates summary statistics for each BAM file specified. The statistics can be found at

${OUT_DIR}/Coverage_Mapping/${PROJECT}_coverage_summary.txt

The original BEDTools histograms can be found in the Histograms directory. Visual diagrams of these histograms are planned for a future version of Coverage_Mapping and will be found under Plots.

Dependencies

Coverage_Mapping depends on BEDTools and R for generating the coverage maps. In addition, PBS and GNU Parallel are required for basic operation. Please check the dependencies page to ensure that you are using the required version of each dependency. Note that Coverage_Mapping is very sensitive to the version of BEDTools.

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