finding SV pipeline with PE reads

[boetsie]

Hi all,

does anyone have a pipeline for finding structural variations on a reference genome using illumina PE reads.

The pipeline would be something like;
- mapping the reads to a reference (bowtie?)
- converting the sam to bam file, and convert to SV detection input format
- SV detection method (Pindel, Breakdancer, CNV-seq...).

Any help on this would be great, especially since there are a lot of issues for inputs for the SV detection methods.

Thanks in advance,
Marten