Question: Which Option Do You Use With Breakdancer?
0
gravatar for madkitty
6.7 years ago by
madkitty570
Canada
madkitty570 wrote:

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 (>.<)

breakdancer cnv • 1.8k views
ADD COMMENTlink written 6.7 years ago by madkitty570
2
gravatar for Niek De Klein
6.7 years ago by
Niek De Klein2.4k
Netherlands
Niek De Klein2.4k wrote:

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
ADD COMMENTlink written 6.7 years ago by Niek De Klein2.4k

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

ADD REPLYlink written 6.7 years ago by madkitty570

what error do you get?

ADD REPLYlink written 6.7 years ago by Niek De Klein2.4k

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..

ADD REPLYlink written 6.6 years ago by madkitty570

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.

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by Niek De Klein2.4k

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

ADD REPLYlink written 6.6 years ago by madkitty570
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