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Old 08-13-2015, 05:56 AM   #1
cmccabe
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Default 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
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Old 08-13-2015, 06:23 AM   #2
GenoMax
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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.

Last edited by GenoMax; 08-13-2015 at 07:45 AM.
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Old 08-13-2015, 07:36 AM   #3
maubp
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There is a BAM to FASTQ function within samtools, available via:

Code:
samtools bam2fq
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Old 08-13-2015, 07:45 AM   #4
GenoMax
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@cmccabe: You will need new version of samtools (v.1.2) for the functionality Peter mentions above.
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Old 08-13-2015, 01:37 PM   #5
cmccabe
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Thank you very much
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