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Old 06-10-2011, 07:06 AM   #1
Location: Fife, Scotland

Join Date: Mar 2010
Posts: 18
Red face pileup2fq problem?


I am new to Samtools, and have a problem which I think must be simple to fix!

I am trying to use the following command on my dataset as per the manual:
$ samtools pileup -cf ref.fa aln.bam | pileup2fq -D100 > cns.fastq

And get the error:
command not found.

I have tried generating the pileup file separately using Samtools which works fine, so I am assuming I have a problem running the perl script? I have downloaded the latest version of Samtools (v0.1.16), so I guess this means I need to download something else/extra component or a specific perl script in order to get this to work?

Any help appreciated!
Lspoor is offline   Reply With Quote
Old 06-10-2011, 09:27 AM   #2
Senior Member
Location: San Diego

Join Date: May 2008
Posts: 912

Do the two parts separately.

You observed that the is by default in the misc folder, not in the same directory as the samtools program itself, right? So probably, the reason it can't find the perl script is because it's not where you told the computer to look.

The script has only one bit that needs to be present to run, Getopt::Std, and I think that's pretty standard. It would tell you that you didn't have it if that were the problem.
swbarnes2 is offline   Reply With Quote
Old 06-10-2011, 09:46 AM   #3
Location: Fife, Scotland

Join Date: Mar 2010
Posts: 18
Default Fixed!

And I just realised if I specified the path to samtools.p it worked! PLease delete my thread as it is no longer needed!
Lspoor is offline   Reply With Quote

pileup2fq, samtools

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