bamAlignCleaner

A simple utility tool to remove references with no aligned reads in a bam/cram file

Installation

• with pip

pip install bamAlignCleaner 

• with conda

conda install -c bioconda bamAlignCleaner

Usage

• Quick start

bamAlignCleaner input.bam

• Advanced

bamAlignCleaner --output output.bam --method parse input.bam

Help

$ bamAlignCleaner --help
Usage: bamAlignCleaner [OPTIONS] BAM

  bamAlignCleaner: removes unaligned references in BAM/CRAM alignment files
  * Homepage: https://github.com/maxibor/bamAlignCleaner
  * Author: Maxime Borry

  BAM: BAM alignment file (sorted, and optionally indexed)

Options:
  --version                       Show the version and exit.
  -m, --method [parse|index_stat]
                                  unaligned reference removal method
                                  [default: parse]
  -o, --output FILE               filtered bam file [default: STDOUT]
  --help                          Show this message and exit.

Methods

bamAlignCleaner uses either one of the two following methods to remove references not having reads mapped against them.

• The parse method goes through each read of the alignment file and keeps the references if the read maps to it. This method should be faster if you have more references than reads.
• The check_index checks index for the number of mapped reads to each reference. This method should be faster if you have more reads than references.

Cite

@software{maxime_borry_2022_6344905,
  author       = {Maxime Borry},
  title        = {maxibor/bamAlignCleaner: bamAlignCleaner},
  month        = mar,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {0.2.2},
  doi          = {10.5281/zenodo.6344904},
  url          = {https://doi.org/10.5281/zenodo.6344904}
}