2.4 years ago by
There are over 50 publicly available structural variant callers, with about 1/4 able to detect small insertions and large deletions using the technique use describe. These include BreakDancer, HYDRA, GASVPro, and CLEVER. Other detection signals that can be used to detect structural variants include read alignment CIGAR, split reads, soft clipped reads, read pairs with only one read mapped, and multiple different assembly-based approaches. Tools using such methods (most of which combine one or more of these signals with read pair information) include Pindel, SRiC, CREST, SVseq2, PRISM, SoftSearch, Socrates, LUMPY, cortex-var, lasSV, AsmVar, SoftSV, manta, and GRIDSS.
I would strongly advise looking at the existing tools and literature before reinventing a wheel.
Disclaimer 1: I didn't check that every one of these tools reports small insertions. Some tools, such as DELLY, use read pair and split read information but do not report insertion events.
Disclaimer 2: As I wrote GRIDSS, it should come as no surprise that I recommend it. My extensive benchmarking shows it outperforms other callers (breakdancer, cortex, delly, hydra, lumpy, pindel, software, tigra) at 15x or greater coverage. That said, if you're interested in novel insertions larger than the library fragment size, you'll need to use a de novo assembly based technique (eg cortex) or a specialised caller such as NovelSeq.