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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. What I want to do is run BreakDancer on both samples and then "subtract" out the variations seen in the normal sample from those in the cancer sample so that I'm left with those specific for the cancer. My problem is how to do this? The results given for each sample are in the form of chr1,pos1,chr2,pos2 as the location of the breakpoints. I've tried to concatenate those values to create a unique identifier for the subtraction, but that did not work very well. How do people do this kind of subtraction to find variations unique to the cancer sample? Is there a better tool than BreakDancer out there for this kind of analysis? Thanks for any help.
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What I've been doing is to expand the calls into regions on each end and writing them out in BEDPE format:
chr1 start1 end1 chr2 start2 end2 strand1 strand2 name etc..
You can do this either by adding a little bit of slop to the location of each breakpoint (i.e. 500bp up and downstream of the location or something similar) or by determining the regions in which the supporting reads for each SV lie using the output file of supporting reads from Breakdancer. Then when I've got a bedpe file, I've been using the pairToPair utility from BEDTools with the "notboth" option to subtract SVs that overlap on both ends. Check out the BEDTools manual for more details on that command.
I think that some of the other SV callers (GASV?) have this sort of capability baked in.
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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