samtools bam2fastq command

[cmccabe]

I have samtools installed to /usr/bin, it was installed using sudo -apt-get install samtools on ubuntu. Is the below command incorrect? Thanks .

 bam2fastq -o IonXpress_009_150603.fq --no-unaligned IonXpress_009_150603.bam
bam2fastq: command not found

[GenoMax]

bam2fastq is not part of new samtools (v.1.2) Peter's post below. It is not in v.0.1.19.

Use bamtofastq from bedtools: http://bedtools.readthedocs.org/en/l...amtofastq.html

Note: How well this will work with a file from Ion you will have to tell us.

[maubp]

There is a BAM to FASTQ function within samtools, available via:

samtools bam2fq

[GenoMax]

@cmccabe: You will need new version of samtools (v.1.2) for the functionality Peter mentions above.

[cmccabe]

Thank you very much