Simple tool to calculate various per-base stats over a bam file, and returns bedgraph files. Currenly only collects stats for depth and mean MAPQ.
Either download prebuilt binaries (Linux x86-64 and MacOS ARM64 only) from the release page: https://github.com/bjhall/bamsta/releases
...or compile from main branch. Requires that the rust toolchain is installed.
git clone https://github.com/bjhall/bamsta.git
cargo build --release
bamsta input.bam output_prefix
PREFIX.dp.bedgraph
- Sequencing depth per base
PREFIX.mapq.bedgraph
- Mean MAPQ per base