Coverage calculator
This repository contains a script to calculate coverage over a BAM file or a list of such files.
Installing
It is advisable to use pip to install the necessary packages. Change into the repository
directory and run
pip install -r requirements.txt
Running
(see script.sh for a usage example)
Output
the script writes a number of files at the given location. these contain sample-wise coverage
statistics as well as cumulative summary statistics. the example_output.png in this repository
shows the list of output files for a run of script.sh assuming bamlist contains three sample
bam files.
the sample##_ files contain individual coverage statistics, the coverage_* files contain
cumulative summary coverage statistics:
*_coverage.mosdepth.* .............mosdepth output files;*_coveragePerBP.bed.gz* ...........mosdepth extra per base-pair output statistics;*_coverageReport* .................sample-wise coverage stats at different aggregation levels;*_lowCoverage* ....................list of sample's regions with reads below the threshold;coverage_* ........................summary of the sample-wise*_coverageReport*files.