BamQVFilter

Installation

Download a ready-to-use binary from the release You may have to change the file permissions to execute it with chmod +x bamqvfilter.

Usage

Filters BAM files based on read quality values.
Options:
  -q, --quality <QUALITY>  Sets a minimum Phred average quality score
  -t, --threads <THREADS>  Use N parallel threads [default: 4]
  -i, --input <INPUT>      Input filename
  -o, --output <OUTPUT>    Output filename
  -h, --help               Print help
  -V, --version            Print version

example:

bamqvfilter -i input.bam -t 24 -q 10 -o output.bam;