bcsubset - BAM file subsetting by barcode

This tool selects a subset of records from a BAM file based on a barcode whitelist.

Input: A BAM file and a barcode whitelist.

Output: A BAM file containing only the records with the barcodes in the whitelist.

Quickstart

Installation

git clone https://github.com/kehrlab/bcsubset.git
cd bcsubset/
make

Execution

Basic execution using default values for trimming (Default: 0) and barcode tag (Default: CB):

bcsubset -w myWhitelist.txt -o outBamName.bam myBam.bam

Setting custom values for trimming and barcode tag:

bcsubset -w myWhitelist.txt -o outBamName.bam -t myNum -b myTag myBam.bam

Note: The whitelist file must contain each barcode in a new line.

Dependencies for Installation via Make

bcsubset has the following dependencies:

• GCC 4.9 or higher
• ZLIB

ZLIB can simply be installed using apt:

sudo apt install zlib1g-dev

Version and License

    Last update: 2021-06-24
    bcsubset version: 0.0.1
    SeqAn version: 2.4.0
    Author: Ana Belen Solis Pinson (ana.pinson[at]bihealth.de)