samtools.pl pileup2fq problem?

[Lspoor]

Hi,

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 | samtools.pl 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!

[swbarnes2]

Do the two parts separately.

You observed that the samtools.pl 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 samtools.pl 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.

[Lspoor]

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!