Delly workflow produces a set of vcf files with different types of structural variant calls: Translocation, Deletion, Inversion and Duplications It uses .bam files as input. The below graph describes the process:
Preprocessing
The expected inputs for the DELLY tool are library-level BAMs with distinct insert size and median. In most cases, this means that the BAM files will not need to be merged prior to processing. However, the DELLY website recommends
This is a companion discussion topic for the original entry at github.com/f73chen/delly/Delly