Detection of fusion from a DNA seq file

Question

[Bioinformatician_in_trouble]

Hi, Can anyone please suggest some free softwares that could help in detection of fusion from a DNA seq file.? Looking forward for response. Thank you in advance.

[WouterDeCoster]

You need to be far more precise when asking questions. Which sequencing technology and which organism? What do you mean with "a DNA seq file"? Is the location of the fusion event a priori known?

[Bioinformatician_in_trouble]

Organism: Human I know the genes that are fused. I have a BAM file that contains the DNA sequence. I tried running TOPHAT fusion but it gave zero fusions. I am not sure how to run Breakdancer, as the perl and cpp version is confusing for me, even after reading the tutorial. TIA.

Answer 1

[Eric T.]

You want a structural variant caller. Consider Lumpy, Delly, Manta, or an ensemble method like MetaSV or Parliament. Your choices also depend on the kind of DNA sequencing you're doing.