How to find structural variants

Question

[897598644]

Excuse me:

By far, I have found snp and indel variants in my whole exome sequencing.

I want to know how to find structural variants in the data.Are there any modules in GATK or third parties tools?

Thx in advance, I will be much appreciated.

Answer 1

[PoGibas]

If you are interested in GATK, this 3 years old answer is what you are looking for. GATK has [Genome STRiP] (http://www.broadinstitute.org/software/genomestrip/genome-strip) tool.

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You can also play around with these tools ( https://www.biostars.org/p/77753/ ) (I would start with delly & pindel).

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You can find even more tools here: Algorithms for the detection of structural variation. (Keane M. et al., "Identification of structural variation in mouse genomes", Frontiers in Genetics, 2014).