Tools to extract coverage informations from BAM (and CRAM) files, based on the covtobed algorithm that supports stranded coverage and physical coverage, input from streams and uses a memory-efficient algorithm.
Full documentation is available online at the dedicated website, or in
this repository under docs.
The BamToCov package is available from BioConda
conda install -y -c bioconda bamtocov- Brent Pedersen, Aaron Quinlan, hts-nim: scripting high-performance genomic analyses (Bioinformatics)
- Giovanni Birolo, Andrea Telatin, covtobed: a simple and fast tool to extract coverage tracks from BAM files (JOSS)