unrecognized command mpileup

[rururara]

Hi,

I'm using samtools 0.1.7.
Suddenly I realized that 'mpileup' command is not recognized and when I checked back the mpileup command is not included in the samtools.
I run this cmd 'samtools mpileup ....' and got error
[main] unrecognized command 'mpileup'
Anyone can explain this? Or should i install the latest one?

Thanks!

[krobison]

Any reason not to upgrade? SAMtools is up to 0.1.13 - I'm guessing mpileup came in after 0.1.7

[Richard Finney]

mpileup appears in samtools-0.1.8

You must upgrade to get mpileup.

From samtools-0.1.8/NEWS:

* Added the `mpileup' command which computes the pileup of multiple alignments.

[rururara]

i tried to upgrade the samtools 0.1.13 but still couldnt find the mpileup.
i'm lost right now to install samtools eventhough i read the installation manual.
can u guys assist me on samtools installation .
may be i miss something during installation.
thanks!

[zee]

Quite straightforward. Install subversion (svn) and do

svn co https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/samtools

A folder named 'samtools' will be created. Every time a new version is released cd to that directory and run

$ svn update
$ make

You can then copy the latest samtools binary to your ${PATH}

[rururara]

thanks all.
btw, success to install samtools.
my mistaked because there is missing library.
i checked back the library and install.
then samtools is ok to use

[qqtwee]

would you like to tell me how do you done it successfully? I have the same error!
Thanks!
Best wishes!

[rururara]

hi qqtwee,


i can't remember as it happen long time ago. but the key is u need to check whether u have the complete library that needed by Samtools to be succesfully installed.
try to read the error log. could be missing some of library from your computer.

good luck!