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-   -   samtools bam2fastq command (http://seqanswers.com/forums/showthread.php?t=61962)

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 :).


Code:

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: 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 08-13-2015 07:36 AM

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

Code:

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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