We're performing NGS on cancer DNA samples with a custom panel of target regions in different genes.
Our structural variants & CNV detection pipeline currently consists of several programs such as Lumpy, Manta, Pindel, Breakdancer, Delly and CNVkit and the variants we're interested in are insertions / deletions (of all sizes), inversions, translocations, CNVs, Internal tandem-duplications and other duplications.
From your experience & knowledge, which tools do you recommend using the purpose of annotation of all sorts of structural variants and CNVs, preferably annotation of VCFs but not necessarily.
Thank you very much in advance! Alon
I realize this has been somewhat asked before but the posts I've found were at least 2-3 years old and didn't elaborate on cancer genomics or exome sequencing.