Where Is Pindel2Vcf

Question

[andrewk]

Hi. I've installed pindel0.2.4t on Ubuntu 10.04.1 LTS using the package in the repository. However I can't seem to locate pindel2vcf which is mentioned several places and in the latest update to the Makefile. Is it supposed to be included in the package or do I need to compile manually to get pindel2vcf?

Thanks!

Answer 1

[John Marshall]

As cwarden45 noted, pindel2vcf is part of the pindel project and comes with it if you build it yourself from the pindel source package.

However WUSTL's pindel binary Debian package contains only pindel0.2.4t and documentation, as you found, and there are no other pindel-related binary packages alongside it, which there might have been if the utilities had been split out of the main package.

So this is an error in packaging. When they made this package, pindel2vcf and sam2pindel were mentioned only in INSTALL and not the Makefile, so it would have been easy to accidentally omit them. As of last week, they have been added to the Makefile. Hopefully WUSTL will update their pindel package to the current version and revisit the packaging scripts to include the associated utilities.

In the meantime, your alternative is to compile pindel2vcf and sam2pindel from source yourself. This is relatively simple as they don't need any third-party libraries; e.g., pindel2vcf can be compiled just with

g++ -O3 pathtopindelsrcdir/src/vcfcreator.cpp -o pindel2vcf

and then you can copy pindel2vcf to somewhere convenient in your $PATH, perhaps $HOME/bin.

[andrewk]

I had a feeling that compiling from source might fix it but thought I would check before doing things the harder way. It was pretty straightforward to use the INSTALL script with a pointer to the samtools path. Thanks.

Answer 2

[Charles Warden]

It is included in the package.

Here is the location for my installation on a Linux server

\opt\pindel-0.2.4\bin\pindel2vcf

[andrewk]

It's not there on my install.

$ ls -l \opt\pindel-0.2.4\bin\pindel2vcf
ls: cannot access optpindel-0.2.4binpindel2vcf: No such file or directory

I've checked the package contents and I get this:

$ dpkg -L pindel0.2.4t
/.
/usr
/usr/share
/usr/share/doc
/usr/share/doc/pindel0.2.4t
/usr/share/doc/pindel0.2.4t/changelog.Debian.gz
/usr/share/doc/pindel0.2.4t/copyright
/usr/bin
/usr/bin/pindel0.2.4t

Doesn't seem to include pindel2vcf. Is the package I have somehow incomplete? I added the WUSTL repository and retrieved from there.

[Charles Warden]

You are using a slightly different version.

I think you would want to check the files within \path\to\pindel\bin. You will need to at least change 0.2.4 to 0.2.4t, but I don't know where you actually installed the program

[andrewk]

Thanks for the help. The version I'm using I installed by following the Ubuntu 10.04 repository install directions on the Pindel main page: http://gmt.genome.wustl.edu/pindel/0.2.4/install.html

I don't see anything in the same place as pindel:

$ which pindel
/usr/bin/pindel
$ ls -l /usr/bin/pindel
lrwxrwxrwx 1 root root 24 2013-11-05 14:16 /usr/bin/pindel -> /etc/alternatives/pindel
$ ls /etc/alternatives/pindel*
/etc/alternatives/pindel

That is why I checked where the package contents were installed using dpkg -L. It seems like only pindel gets installed. Does anyone have pindel2vcf installed from using the Wash. U. repository as detailed in the install page?

[Charles Warden]

I believe it was installed with similar instructions (but for a little different version). I had to have a system admin install the program on the shared instructions, but that was the website that I provided.

Maybe you'll have to contact one of the developers. The only other thing I can think of is that Pindel also has a sourceforge site (but I think it has less documentation):

http://sourceforge.net/projects/pindel/?source=directory

Answer 3

[liangkaiye]

github.com/genome/pindel is the official site. sourceforge is outdated and never updated. the latest version is 0.2.5. pindel2vcf is compiled together with rest of the code.