Coverage Blind Spots

This software lists all positions in given bam files, that have no or only very limited coverage and stores the result in a hdf5 file.

Usage

cbs [-h] [--min-cov MIN_COV] files [files ...] output

If multiple files are given, a position is designated a blind spot, if no file contains a coverage of at least MIN_COV at this position.

Output

The output is a hdf5 file with the following structure. For every chromosome a group is created, that contains a dataset called missing_cov. The dataset contains rows of tuples of 32bit integer, representing the first blind spot and the first position having enough coverage.

Install

This software requires python3, samtools, hdf5, numpy and h5py. All python dependencies can be installed by installing cbs via pip:

pip install git+https://github.com/christofsteel/cbs.git