Which Option Do You Use With Breakdancer?

Question

[madkitty]

Which option do you use with Breakdancer ? I usually write no options like that

perl bam2cfg.pl input.bam > input.cfg
breakdancer input.cfg > output.txt

I saw that some experts use the -g and -h options, I've read the readmefile and I still don't understand what difference does it make..

If you want to have CNV Gain AND Loss from paired-end sequencing which option would you use ?

ps : I'm a breakdancer newbee (>.<)

Answer 1

[Niek De Klein]

Read the usage page. It explains all the options.

-g FILE   dump SVs and supporting reads in BED format for GBrowse
-h         print out Allele Frequency column, by default off

[madkitty]

thanks but -h doesn't work for me it prints out an error message

[Niek De Klein]

what error do you get?

[madkitty]

If I just type in perl bam2cfg.pl -g -h myfile.bam > myfile.cfg

I have the following error : Use of uninitialized value in printf at bam2cfg.pl line 222.

I checked at line 222 and here is what I have : printf "%d",$flagHgram{$rg}{all};

I'm clueless..

[Niek De Klein]

arggh I was sleeping when I wrote this, I meant: Try perl bam2cfg.pl -gh myfile.bam > myfile.cfg. So both letters with one stripe. Also, just saw I linked to the wrong usage page. For bam2cfg.pl look at http://breakdancer.sourceforge.net/bam2cfg.html.

[madkitty]

bam2cfg doesn't work without writing 'perl' before it. I think there's something to modify in the code of bam2cfg but I know nothing about perl .. Anyway Thanks