Bam2Fastq on Helix
BAM-format files are used to store alignment information and unaligned reads from next-generation sequencing machines. This tool is intended to extract raw sequences (with qualities) from a BAM file.
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
[user@helix]$ module avail bam2fastq ----------------------------- /usr/local/Modules/3.2.9/modulefiles -------------------------- bam2fastq/1.1.0 [user@helix]$ module load bam2fastq [user@helix]$ module list Currently Loaded Modulefiles: 1) bam2fastq/1.1.0 [user@helix]$ module unload bam2fastq [user@helix]$ module load bam2fastq/1.1.0 [user@helix]$ module list Currently Loaded Modulefiles: 1) bam2fastq/1.1.0 [user@helix]$ module show bam2fastq ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/bam2fastq/1.1.0: module-whatis Sets up bam2fastq 1.1.0 prepend-path PATH /usr/local/bam2fastq -------------------------------------------------------------------
Sample session on Helix
$ module load bam2fastq $ cd /data/$USER/mydir $ bam2fastq --aligned -o myfile.fastq myfile.bam
Documentation
http://www.hudsonalpha.org/gsl/information/software/bam2fastq
