BamCmp

bamcmp is a command-line tool for comparing two alignment files that contain the same alignment data. For example, two alignments that are in BAM and SAM format, or BAM and CRAM format.

Installation

To install the command, first ensure you have Python 3.7 or above installed. Then, run:

python3 -m pip install git+https://github.com/TMiguelT/BamCmp

Usage

Once you install this package, you will have the bamcmp command available.

The full command line interface, including additional flags, is listed here:

usage: bamcmp [-h] [--reference REFERENCE] [--ignore-tags] [--sort-tags]
              bam_a bam_b

positional arguments:
  bam_a
  bam_b

optional arguments:
  -h, --help            show this help message and exit
  --reference REFERENCE
                        Path to reference fasta file, needed for CRAM
                        alignments
  --ignore-tags         Ignore the optional tags section for each segment
  --sort-tags           Sort tag dictionary before comparing, meaning that
                        alignments with differently ordered tags will still be
                        considered identical