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Old 12-12-2011, 09:02 AM   #41
aquinom85
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Hey MJ,

Does Breakway detect copy change, inversions, translocations, or rearrangements? Also does it report on the zygosity of the SVs it detects and is it able to jointly call samples?

-Mark
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Old 12-12-2011, 01:33 PM   #42
Michael.James.Clark
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Hi Mark,

Breakway will call five types of SVs:
Deletions
Insertions
Interchromosomal Translocations
Intrachromosomal Translocations
Inversions

Copy changes are typically going to fall under one of these classes. Breakway does call Indels by looking at the copy state of the region between the ends of an SV call. So in that sense, it calls copy changes. However, it does not call CNVs (nor does any other SV algorithm I know of). Rather, CNVs are typically called with another algorithm or program and then cross-referenced with the SV list. You can do this with Breakway using any CNV program (like CNVnator).

As for zygosity, the copy number of indels is determined by comparison with the local sequence context. So yes, zygosity can be determined from it--e.g. a deletion in a diploid region is going to result in a homozygous region.

Breakway calls one sample at a time, but of course it can be run in parallel on multiple samples, etc. It does not leverage SV calls across samples (though that would be a fantastic addition to this or another program--I am not aware of a SV program that does this).

MJ
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Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
Projects: U87MG whole genome sequence [Website] [Paper]
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Old 12-12-2011, 01:53 PM   #43
aquinom85
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Thanks for getting back to me so quickly and clarifying those points MJ. FYI PennCNV and GASV jointly call samples, it seems like a hard-to-find feature but they do exist!

-Mark
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Old 12-12-2011, 02:01 PM   #44
Michael.James.Clark
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I don't think PennCNV is a SV algorithm, is it? I mean, CNVs are technically SVs, but it's a CNV program isn't it? Or does it call things like translocations and indels?

GASV I haven't used, so I can't comment beyond their paper. It does indeed work with multiple samples (in fact, that's a major benefit to it), but my understanding is that it doesn't empirically determine SV boundaries. I don't really know, though, so definitely look into it!

To the question of how to generally approach SV detection, my advice to you based on what we do here at Stanford is to use multiple algorithms, weight their scores based on their strengths and strategies, and combine the results.
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Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
Projects: U87MG whole genome sequence [Website] [Paper]

Last edited by Michael.James.Clark; 12-12-2011 at 02:02 PM. Reason: Added some clarification.
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Old 12-13-2011, 07:06 AM   #45
aquinom85
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I believe you are correct about PennCNV, I just briefly checked what it's input is (probe intensity data) and based on that I can't imagine it's able to actually call anything but copy number variation. My mistake.
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Old 03-22-2012, 01:48 AM   #46
dnusol
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Hi MJ,

what kind of length range can Breakway detect with paired-end data? large INDELS (upto 1Mb or so)?

Cheers,

Dave
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