Hi everyone,
I have 4 samples (matepair illumina) and run Breakdancer_max as follows:
bam2cfg.pl -h -g -q 10 sample1.bam sample2.bam sample3.bam...
20 results in 0.0022 seconds.
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Breakdancer Output in multisample problem
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Breakdancer inaccurate output.
Hi Guys,
I have run Breakdancer on a mouse KO sample and got several lines containing intrachromosomal translocations but described as interchromosomal,... -
Error: Running pindel on breakdancer output
Hi All,
I am running breakdancer output in pindel and getting errors. My command is as follows:
pindel -f human_g1k_v37.fasta... -
Breakdancer SV Questions
These might be very simple questions, but I am new to looking at breakdancer output files, and I am having a little trouble interpreting orientation of... -
Breakdancer installation problem
Hi,
I was trying to install the latest version of breakdancer tool (breakdancer-1.1.2_2013_03_08). However, the compilation with cpp version... -
Breakdancer bam2cfg.pl emtpy output with multiple readgroups
Hallo everyone,
This has been bugging me for a few days now, I get empty output from bam2cfg.pl from my merged bam file. I've seen many... -
Tigra-sv output
Question about output
Hello,
I have one output file from breakdancer, then, as I have multiples breakpoints... -
Filtering Breakdancer results
Hello,
I am trying to use breakdancer for the first time, and I am wondering about rational strategies for trying to filter down to the most likely... -
breakdancer several bam misunderstand
Hello,
I am calling breakdancer to see which structural variants are different from one sample to another. For these I do this two steps:... -
What's wrong with my pipeline of BreakDancer?
Hello! I am new in this research region. I try to use breakdancer to detect the SVs. I process the following steps:
1. I wrote a program... -
Misunderstanding breakdancer output
Hello
I am running breakdancer for my samples and I get some results that I don't understand.
For example I get these:
1.... -
BreakDancer - Cancer/Normal Matching
Hi. I'm using BreakDancer to find structural variations in a paired set of samples. One sample is a tumor and the other is the matched normal sample.... -
how to do annotation on Breakdancer result
I've got some breakdancer results on SV. But the format is not in VCF. Beside, the outcome of breakdancer is an estimate of structural variation. It couldn't... -
BreakDancer empty cfg (no output from bam2cfg)
Hi, everyone, I had spent days to do trouble-shooting on bam2cfg.pl,
breakdancer-1.1_2011_02_21.zip. I had tried some ways to figure out the problem,...Last edited by zhongj; 12-14-2011, 01:50 AM. -
Structural variation detection using BreakDancer on Whole Genome SOLiD data
Hello,
I have been struggling for the last few weeks to get Breakdancer to run accross some whole genome data. The data was sequenced...
