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Simple convertor from bam to FASTQ
C++ Makefile
Branch: master
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Latest commit 0764cd0 Jun 30, 2015
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samtools @ 28391e5 added samtools as a submodule Apr 11, 2014
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HISTORY.txt initial import Apr 11, 2014
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Makefile added samtools as a submodule Apr 11, 2014 Fixed broken link Jun 30, 2015
bam2fastq.cpp implement writing to stdout Apr 11, 2014


bam2fastq is a program to extract sequences and qualities from a BAM file.

The original version can be found here. It has subsequently been modified to handle BAM files with mixtures of paired and unpaired reads and write to stdout.


Requires make, gcc, and the zlib compression libraries - all of which should be present on most Unix-like systems (including Macs).

First clone the repository from github, including its dependencies:

git clone --recursive

Then change to the directory and run make:

cd bam2fastq


This program was originally developed at HudsonAlpha by Phillip Dexheimer. It was packaged on github and slightly modified by Jared Simpson.

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