Structural Variants

[jkozubek]

Hello all:

I interested in what tools people have found easiest and useful for detection of structural variants (including indels, inversions, translocations).

Jim

[jorhodes]

You could try Breakdancer (http://breakdancer.sourceforge.net) which is good for detecting chromosomal translocations

[vivek_]

There's several options but the choice depends on what kind of data you are working with. For exome data with paired end reads, split read methods like breakdancer might be the best option while other tools like CNVnator etc that use a read depth approach can be used on whole genome data.

[prathima]

Structural Variants in Strand NGS software

Detection of Structural Variants in Targeted Sequencing application is possible with Strand NGS software which might be of interest to you.
Recorded webinar is available at:
http://www.strand-ngs.com/learn/webinar-recordings

For more details on DNA Seq features: http://www.strand-ngs.com/features/dna-variation

[GenoMax]

@prathima: If you are going to keep posting on behalf of Strand Genomics then you may want to get "Registered Vendor" status by emailing admin at seqanswers dot com.

You also should also mention that Strand NGS is non-free commercial software when mentioning it as an option.