This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Bam2Cfg.Pl And Breakdancer

We have a whole genome sequence data on BAM file and want to detect INTER AND INTRA chromosomal rearrangement. I need to create a config file to use with breakdancer. The config files are create with bam2cfg.pl.

  • PROBLEM #1

This bam2cfg.pl. software has a lot of options and I'm not familiar with it. If I do the following command : 

 perl  bam2cfg.pl. myfile.bam > myconfigfile.cfg   #This works well

 perl bam2cfg.pl. -g -h myfile.bam > myconfigfile.cfg     #This doesn't work and returns..

 Use of uninitialized value in printf at bam2cfg.pl line 222.
  • PROBLEM #2

We want to identify CNV Loss and Gain with Breakdancer, but when I look at the pipeline it only gives an example for inter-chromosomal rearrangerement. Which options should I use with bam2cfg.pl. and breakdancer to have CNV Loss and Gain ?

breakdancer cnv
• 3,722 views • link
written by madkitty madkitty

Would you please share your experience on how you ended up (the parameters) using breakdancer.

• 0 views • link
written by Chirag Nepal Chirag Nepal

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Error Running Breakdancer-Max: Max Kahan Error: 0
    written by tptacek3050 tptacek3050
    <p>This is a re-posting of an older topic that I have still not resolved. This was covered in <a href='http://www.biostars.org/p/85056/'>these</a> <a href='http://www.biostars.org/p/85989/'>two</a> prior threads. In …
  • Error Running Breakdancer-Max: Max Kahan Error: 0
    written by tptacek3050 tptacek3050
    <p>I'm attempting to run breakdancer-max, and am running into an error that I can not find documentation on. My script looks like this:</p> <p>=======</p> <pre><code>#breakdancer …
  • Breakdancer -Q Flag Doesn'T Work
    written by madkitty madkitty
    <p>for some reason I just found out that whatever value enter after -q flag in breakdancer returns an empty file. Did anyone ever experienced that …
  • Breakdancer Options, Unconsistency Please Help!
    written by madkitty madkitty
    <p>I want to run a CNV call with breakdancer, so I tried two methods :</p> <p>1) Using AWK to select only reads that have a …
  • Breakdancer Output : What'S Wrong With This Query ??
    written by madkitty madkitty
    <p>I ran Breakdancer on a sample dispatched into 4 bam files. Where options -g -h are set an error message shows up : </p> <pre><code>perl …
  • Ideogram Cnv With Bioconductor Does That Look Good ?
    written by madkitty madkitty
    <p>I have generated an ideogram of Chromosome 1 of our first sample, the annotation are CNVs identified found in this sample with Breakdancer. Here is …
  • Multiple Samples Data And Chromosome Ideograms From Cnv Caller
    written by madkitty madkitty
    <p>I have posted a similar question here : <a href='http://www.biostars.org/post/show/46740/how-to-create-such-figure-of-chromosomes/#46762'>http://www.biostars.org/post/show/46740/how-to-create-such-figure-of-chromosomes/#46762</a></p> <p>An other similar figure representing multiple samples ideograms can be found here : <a href='http://www.biostars.org/post/show/378/drawing-chromosome-ideogams-with-data/'>http://www.biostars.org/post/show/378/drawing-chromosome-ideogams-with-data/</a></p> …
  • Breakdancer False Positive
    written by madkitty madkitty
    <p>We performed and whole genome sequencing with NGS, and used Breakdancer to detect Copy Number Variation. Breakdancer and config files were made with NO options …
  • Which Option Do You Use With Breakdancer?
    written by madkitty madkitty
    <p>Which option do you use with Breakdancer ? I usually write no options like that </p> <pre><code>perl bam2cfg.pl input.bam &gt; input.cfg breakdancer input.cfg &gt; output.txt …
  • Breakdancer And Bam2Cfg.Pl
    written by madkitty madkitty
    <p>We have whole genome sequencing file aligned into a bam format file. Each sample has at least 2 bam files. </p> <p>I want to find …