bamAlignCleaner 0.2

Removes unaligned references in BAM alignment file

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 -c conda-forge -c maxibor 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 (indexed and sorted)

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.