Breakdancer And Bam2Cfg.Pl

Question

[madkitty]

We have whole genome sequencing file aligned into a bam format file. Each sample has at least 2 bam files.

I want to find CNV Gain and Deletion from those bam files with Breakdancer, but I need to create a configuration file with bam2cfg.pl

They said I have to type : bam2cfg.pl -q [BDmapq] -n [readsToSample] bamfile > bd.config

How do I know BDmapq? How do I know readsToSample?

What's "bamfile" ? Is it the path to my bam file ? What's "bd.config" ??

Let's I have the following bam file /home/myfile.bam /home/myfile.bai

What do I do from here ??

Answer 1

[Mike Smith]

"BDmapq" is an integer specifying the minimum mapping quality for a read to be used by the algorithm.

"readsToSample" is also an integer, this time giving the number of read pairs that should be used to estimate the insert size of your library.

However, you can omit both and Breakdancer will use its default values. You can find a few more details of the arguments here: http://breakdancer.sourceforge.net/bam2cfg.html

The "bamfile" argument is a space separated list of the bam files you want included. You say you have at least two bam files per sample, so you probably want something like: /home/myfile1.bam /home/myfile2.bam

The final part, "bd.config", is the name of the config file to be created. if you don't include it the resulting config information will be printed to the screen. Using ">" will direct that to the specified file, rather than the screen.

[madkitty]

Thanks for your answer. I tried with all the values and now it says "Can't locate GD/Graph/histogram.pm in @INC" ..

[J.Rodrigo Flores]

Hi,

Then you have to install that module. You can find it (and plenty more of them) in the CPAN Repository. The one you're lookin for is this

http://search.cpan.org/~lds/GD-2.46/GD.pm

There are some alternative (and faster) ways to install a CPAN Module but if you haven't done it before I'd suggest the manual installation. Googling you can find lots of help for doing this. Like this link.

http://www.thegeekstuff.com/2008/09/how-to-install-perl-modules-manually-and-using-cpan-command/

A common problem in not having permissions to install modules on the system so you have to install it locally in your directory and then tell the system where to find that module. In oder words, include the folder where you installed the module in your $PATH. Some guidelines here

http://www.perlmonks.org/index.pl?node_id=128077