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cmccabe 08-13-2015 05:56 AM

samtools bam2fastq command
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 08-13-2015 06:23 AM

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:

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

maubp 08-13-2015 07:36 AM

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


samtools bam2fq

GenoMax 08-13-2015 07:45 AM

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

cmccabe 08-13-2015 01:37 PM

Thank you very much :)

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