How can I run 'mpileup' using Bioperl ?
When trying to run mpileup using Bio::Tools::Run::Samtools , I am getting 'mpileup' is not registered. What am I doing wrong? Any pointers towards the right direction are appreciated... thank you guys.....
Asked
Active
Viewed 345 times
1 Answers
2
The short answer is you cannot run mpileup using BioPerl-Run because, as your error message describes, that command does not appear to be listed as one available to samtools. You might want to raise this issue on the bioperl-listserv, and hopefully someone will add this feature.
SES
- 850
- 1
- 9
- 21
-
Oh OKAY...THANK YOU ....are there any other variant calling programs available that can be run through Bio-Perl? – yathrakaaran Apr 01 '13 at 18:18
-
Unfortunately, I don't think there are at this time. One of the difficulties is that this is a rapidly changing field and I don't think many people are eager to try and maintain wrappers for these programs because of that. Please consider upvoting and/or accepting the answer, thanks. – SES Apr 01 '13 at 21:29
-
Thank you so I guess I have to write my own. The problem I can't even install wrapper maker for Bio-Perl are there any tutorials to install them properly?....I am using C-Pan but it is not recognizing the file to install.. To up vote - I tried but couldn't since there is something about 15 reputations. How do I accept your answer? – yathrakaaran Apr 02 '13 at 00:36
-
Okay ....what I really meant to ask was how to install Bio::Tools::WrapperMaker ? Where Do we find it from ? When I do i/Bio::Tools::WrapperMaker/ in CPAN, it says object not found. I have the latest version of BioPerl installed. – yathrakaaran Apr 02 '13 at 07:38
-
I think you might be looking for module that doesn't exist anymore. Take a look at the [Wrappers HOWTO](http://www.bioperl.org/wiki/HOWTO:Wrappers) for some pointers. Sorry about the comment, I forgot you can't up vote. You should be able to click the check mark next to the score and accept the answer though. – SES Apr 02 '13 at 12:21