A Platypus-based insertion/deletion-detection workflow with extensive quality control additions for the workflow management system Roddy. The workflow is only suited for human data (hg37/hg19; some later versions also hg38), because of the big role annotations play in this workflow.
The indel pipeline detects high confidence indels (1-20 bp). The results are presented in an extensively annotated VCF file. The input of the pipeline are the aligned tumor and control bam files. To enable a fast quality assessment of functionally indels screen shots are taken of exotic high confidence indels.